An Introduction to Cookie Science: Nerds Bake Better Cookies

Most traditional chocolate chip cookie recipes start with the same basic ingredients and the same basic technique: cream room temperature butter and a mix of granulated and brown sugar together with a touch of vanilla until fluffy, eggs are beaten in one at a time, followed by sifted flour, salt, and some sort of chemical leavening agent (baking soda, baking powder, or a bit of both). The mixture is combined just until it comes together, then spooned onto a baking sheet and baked.

According to Nestlé, the Toll House recipe originated with Ruth Wakefield who, along with her husband, operated a lodge in New England called the Toll House Inn. Sometime in the early 1930’s, Ruth was preparing cookies for her guests when she chopped up a bar of Nestlé Semi-Sweet chocolate and added it to the dough. The result became the most popular chocolate chip cookie recipe in the world. By 1939, Nestlé began producing the Toll House Morsels to make it easy for everyone to make this recipe.

If you have followed the famous Nestle Chocolate chip cookie recipe on the bag, you have done this. Probably countless times.

When you bake a cookie, here’s what’s going on, step-by-step:

  1. The dough spreads: As the butter warms, it slackens. The cookie dough begins to turn more liquid and gradually spreads out.
  2. The edges set: As the cookie spreads, the edges thin out. This, coupled with the fact that they are fully exposed to the heat of the oven and are constantly reaching hotter areas of the baking sheet, causes them to begin to set long before the center of the cookie does.
  3. The cookie rises: As the butter melts and the cookie’s structure loosens, this frees up water, which in turn dissolves baking soda. This baking soda is then able to react with the acidic components of brown sugar, creating gases that cause the cookies to rise up and develop a more open interior structure.
  4. Egg proteins and starches set: Once they get hot enough, egg proteins and hydrated starches will begin to set in structure, finalizing the shape and size of the finished cookie.
  5. Sugar caramelizes: At its hottest areas—the edges and the underbelly in direct contact with the baking sheet—sugar granules melt together, turning liquidy before starting to caramelize and brown, producing rich, sweet flavors.
  6. The Maillard reaction occurs: Proteins in the flour and the eggs brown, along with the sugar, in a process called the Maillard reaction—the same reaction responsible for giving your hamburger or bread a brown crust. It produces nutty, savory, toasted flavors.
  7. The cookie cools: Once it comes out of the oven, the process isn’t over yet. Remember that liquefied sugar? Well as the cookie cools, that liquid sugar hardens up, which can give the cookie an extra-crisp, toffee-like texture around the edges. Meanwhile, the air in the center cools, which causes the cookie to deflate slightly; though when fully baked, the structure lent by eggs and flour will help it retain some of its rise.

It’s a simple technique that hides more complicated processes underneath. So how do you decipher what’s going on? Test out each basic ingredient one at a time in order to determine how they affect the final outcome.

We’re going to look at many of these alternatives and explain how changing any element – no matter how small! – can drastically change your end result.

Butter: How to Change a Cookie’s Flavor and Texture

Cookie Fact #1: More Butter = Wider Spread and More Tenderness

First, butter keeps cookies tender. When flour is mixed with water (such as the water found in eggs), it develops gluten, a tough, stretchy network of interconnected proteins that set up as they bake. Gluten forms slowly (or not at all) in fat, thus butter will inhibit the cookie’s overall formation, leading to more tender results. The higher the proportion of butter to other ingredients, the more tender your cookie will be (and consequently, the more it will spread as it bakes). 

A ratio of 1 part flour to 1 part sugar to 0.8 parts butter is about right for a cookie that has moderate spread and doesn’t end up cakey.

Because of shortening’s different melting qualities (and the fact that it has no water content), shortening-based cookies come out softer but more dense than those made with butter.

Cookie Fact #2: Creamed Butter = Lighter and Firmer Cookies, Melted Butter = Denser and Chewier Cookie

How butter is incorporated can also affect texture. In the early creaming stages of making a cookie, cool butter is beaten until it’s light and fluffy. During the process, some air is incorporated and some of the sugar dissolves in the butter’s water phase. This air in turn helps leaven the cookies as they bake, giving them some lift. Melting butter before combining it with sugar and eggs leads to squatter, denser cookies.

Cookie Fact #3: Butter Gives the Most Flavor

Butter is essential for flavor. Substituting butter with a less flavorful fat like shortening or margarine yielded sub-par cookies. Butter is about 80 to 83% butterfat, 15% water, and 3 to 5% milk protein. These proteins brown as the cookie bakes, adding nuttiness and butterscotch notes to the final flavor of cookies.

Cookie Fact #4: Browned Butter = Less Moisture and Less Dissolved Sugar = Less Caramel Flavor

If browning milk proteins provide extra flavor to cookies, how could we boost that flavor? Charles Kelsey, the man behind the sandwich shop Cutty’s, developed a simple chocolate chip cookie recipe for Cook’s Illustrated magazine back in 2009. In his recipe, he made the ingenious discovery that browning the butter before adding it to the mixture would give the cookies a much more pronounced nuttiness.

But this created problems. Since the butter can’t get hot enough to brown milk proteins until all of its water content has evaporated, brown butter adds no moisture to dough. This produces a couple of interesting results. Without water, sugar that is mixed into browned butter cannot dissolve (sugar molecules are highly hydrophilic and will dissolve readily in water, but not in fat), which makes it subsequently more difficult for them to melt into each other as the cookie bakes.

With less water, you also end up with less gluten development, thus a cookie made with browned butter is softer and more tender than one made with creamed or plain melted butter. 

So how do I get the flavor benefits of browned butter while still allowing for sugar to dissolve and caramelize properly? The answer turned out to be in the eggs.

Eggs Affect the Shape and Texture of Cookies

Egg whites provide a good amount of water, as well as protein. Egg proteins are particularly good at trapping and retaining bubbles of air or water vapor. The higher the proportion of egg white in a cookie, the more it rises during baking. Because of the extra water, you also get more gluten formation, which again leads to a taller cookie (provided you use enough flour to absorb that extra water). Other than the small amount in the butter, eggs are the main source of water in a cookie dough recipe.

Egg yolks also provide some moisture and protein, but more importantly they provide a well-emulsified source of fat. When cooked, egg yolk forms a tender protein coagulum that can keep cookies tender and fudge-like. A high proportion of egg yolk leads to a more brownie-like texture in a finished cookie.

Cookie Fact #5: Extra Egg Whites = Taller Cookies. Extra Egg Yolks = Fudgier Cookies

By keeping the total mass of egg added to a dough the same but altering the proportion of white to yolk, you can achieve a variety of textures. Two whites and a yolk, for instance, produces the more open structure of the top cookie in the photo below, while three yolks and no whites produces the denser, fudgier texture of the cookie on the bottom.

Turns out that the combination that works best is actually a 1:1 ratio of egg whites to egg yolks, which conveniently is exactly how eggs naturally come. Ain’t that something?

Cookie Fact #6: Too Much Dissolved Sugar = Uniform Texture and Less Cracking

Going back to the initial problem of wanting the flavor of browned butter but disliking the way it prevented sugar from properly dissolving, we might come to this solution: what if instead of creaming sugar and butter and adding eggs, we beat together the eggs and sugar and THEN then add the butter?

In other words, what if we beat brown sugar, granulated sugar, and vanilla with whole eggs in a stand mixer until the mixture became pale, aerated, and ribbony, with a *nearly* completely smooth texture. THEN add our cooled browned butter.

*A sugar and water solution becomes fully saturated at room temperatures at a ratio of about 2 parts sugar by mass to 1 part water (that is, you can’t dissolve any extra sugar because it will stay granular). This recipe experiment contained about 4 ounces of egg and 10 ounces of sugar, so perfect smoothness was an impossible goal.

The end result works okay, but it has an oddly uniform surface with no real textural interest. Turns out you need a balance between dissolved sugar and undissolved sugar.

Cookie Fact #7: The Warmer the Butter, the Denser the Cookie

Here is the next step: beat half of the sugar with the eggs until it completely dissolved, then incorporate the rest when adding the cooled brown butter. The degree to which the butter is cooled before adding it to the mix can also affect how well it holds air when being mixed with the eggs. Why? Warm butter flows very easily and doesn’t trap bubbles well. The cooler it is, the more viscous it becomes, and the better it can trap air. Even a few degrees can make a difference. By letting our browned butter cool down until it is almost at room temperature, it becomes firm enough to beat into the egg and sugar mixture without deflating it.

Sugar: A Mix Provides Balance

There’s more to sugar than just sweetness! The type of sugar you use and its method of incorporation can have a profound effect on the finished cookies. 

Cookie Fact #8: Granulated Sugar = Thin and Crisp, Brown Sugar = Tall and Moist

Granulated sugar is crystallized sucrose, a disaccharide consisting of a fructose molecule and a glucose molecule linked together. It is mildly hygroscopic (that is, it likes to retain moisture), and relatively neutral in pH.

Brown sugar is mostly crystallized sucrose, but also contains a good amount of glucose and fructose, along with trace minerals that give it its flavor and a slightly acidic pH. Glucose and fructose are far more hygroscopic than sucrose.

Check out what happens if you bake cookies that are made 100% with granulated sugar or brown sugar:

You can clearly see the difference in spread. This happens because the baking soda in the cookie recipe is a powdered base, and needs some form of acid to react in order to create the bubbles that leaven the cookie. Slightly acidic brown sugar causes cookies to rise higher when baking, which limits their spread. You end up with a cakier end result. Granulated sugar, on the other hand, adds no leavening power, so you end up with a cookie that spreads wide. Because granulated sugar-based cookies more readily give up moisture, they also end up more crisp.

A mixture of the two provides a good balance, and as we know from the egg experiment, dissolving too much sugar can lead to a texture that’s too uniform. With sugar left in distinct grains, the pockets of melted sugar that caramelize within the cookie as it bakes remain irregular, giving the cookie more textural interest.

But brown sugar has another advantage over granulated: it caramelizes more readily, leading to more intense flavor.

Cookie Fact #9: Corn Syrup = Soft, Wide, Dark, and Flexible Cookies

Incidentally, if you want the absolute chewiest, most uniformly textured cookies, try replacing some of the granulated sugar with corn syrup, a sugar that is even more hygroscopic. You end up with wide, flat cookies that stay soft and flexible even when completely cooled. Not only that, but since corn syrup is made up of simple sugars, it caramelizes more readily, leading to darker overall color.

Corn syrup is so darn powerful, in fact, that even a small amount of it will completely alter the texture of your cookie. In the cookies above, the batch on the left was made with 5 ounces each of granulated and brown sugar. The batch on the right was made with 5 ounces of brown sugar, 4 ounces of granulated sugar, and 1 ounce of corn syrup — a substitution of only 10%.

Next up: baking soda and baking powder.

Choice of Leavening Changes Cookie Texture and Color

Leavening—the introduction of air to the internal structure of baked goods—can come in many forms. In bread, it’s the carbon dioxide produced by yeast. In a cream puff, it comes from expanding water vapor. In the case of cookies, we get it from egg proteins capturing expanding gases, creamed butter, and most importantly, chemicals, namely baking powder and baking soda. What’s the difference between the two?

Cookie Fact #10: Baking Soda = Craggy and Coarse, Baking Powder = Cakey and Smooth

Baking soda is pure sodium bicarbonate—an alkaline powder (a.k.a. a base). When dissolved in liquid and combined with an acid, it rapidly reacts, breaking down into sodium, water, and carbon dioxide.

Baking powder, on the other hand, is baking soda with powdered acids built right in. In its dry state, it’s totally inert. But once you add a liquid, the powdered acid and base dissolve and react with each other, creating bubbles of carbon dioxide without the need for an external acid source. Most baking powders these days are double acting, which means that they contain two different powdered acids. One reacts immediately upon mixing with water, and another only reacts after it’s heated, giving cakes and cookies a little boost early on in the baking phase.

Making cookies with varying degrees of both soda and powder, I found that baking powder generally produces cakier cookies that rise higher during baking, producing smoother, shinier tops, while baking soda yields cookies that are wider, flatter, craggier and denser in texture

Few people want “cakey” chocolate chip cookies, so baking powder is unnecessary. After all, the brown sugar provides plenty of acid for the baking soda to react with. Moreover, because the Maillard reaction takes place more readily in mildly alkaline environments, baking soda has a powerful effect on how rapidly foods darken and develop browned flavors. Browning is a good thing when it comes to cookies.

Flour Is All About Cookie Structure

Cookie Fact #11: More Bread Flour = Chewier Cookies, More Cake Flour = Softer Cookies

The main difference in flour varieties comes down to protein content. Cake flour contains a relatively low amount, which leads to less gluten formation. Cookies made with all cake flour will be very soft, almost mushy, even when you’ve cooked them to what would normally be a beyond-crisp stage. Cookies made with all bread flour, on the other hand, come out ultra-chewy. 

Cookie Fact #12: Less Flour = Lacier Cookies, More Flour = Doughier Cookies

Since flour provides the bulk of the structure in a cookie, the amount you use can alter the texture of the cookie. A small amount of flour compared to butter (a ratio of 1 to 1 or less) will give you cookies that spread out into a wafer-like lace cookie. Extra flour (a ratio of 1.3 to 1 or higher) will give you cookies that barely spread at all as they bake, with centers that stay dense and dough-like, even after being almost fully cooked.

Cookie Fact #13: Less Kneading = Craggier Cookies and Better Texture

Turns out that how you incorporate that flour also makes a difference. (Are you sensing a theme here? When it comes to cookies, apparently EVERYTHING MATTERS.)

The dough above was made by really working the flour into the butter and egg mixture before subsequently folding in the chocolate chips. As you can see, it comes out very smooth and it bakes into correspondingly smooth cookies. Because extra kneading creates a stronger gluten network, the cookies also end up rather tough.

Much better is to barely work the flour in, folding it or mixing it with a stand mixer until it just pulls together into a dough. I incorporate the chocolate half way through this process, so that I don’t accidentally overmix the dough while trying to fold the chocolate in.

The resultant scoops of dough should have a natural cragginess to them even before baking.

If you like extra craggy cookies, Baking Illustrated offers a neat tip for increasing that cragginess: tear the balls of dough apart with your fingertips and smoosh ’em back together with the jagged torn part facing outwards.

Provided you’ve used enough flour and your other ratios are spot on, those crags should appear in the cookies’ final baked form.

Making extra craggy surfaces on cookies the “Baking Illustrated” way

Chocolate Isn’t Just About Flavor

When it comes to the final product and the type of chocolate you use, lots of amateur bakers think that the only real question is brand and cacao percentage – ie milk, semisweet, or dark chocolate.

Dark and milk chocolates are made up of cocoa solids (also called cocoa liquor), cocoa butter, sugar, and flavouring such as vanilla. Milk chocolate is milder than dark chocolate because it has fewer cocoa solids and more sugar and cocoa butter, making it melt more easily and taste a little sweeter. Do you want a bittersweet bite? You’re looking for a medium cacao percentage – about 40 – 62%. Like it dark? 63-90%.

Before we talk about why the way you ADD chocolate to your cookie dough is important, let’s spend a minute on the chips versus discs versus chopped chocolate debate.

Chocolate chips and morsels are essentially the same thing: bits of chocolate designed to hold their shape in the hot oven, not melt into a puddle of deliciousness. They have less cocoa butter than “eating chocolate” or “baking chocolate” (the cocoa butter/ fat is what is actually doing the melting) and have a couple of extra things added: stabilizers such as soy lecithin, to help them keep their shape while baking and melting. I used to think that morsels contained wax or had been pre-cooked. Turns out this was a rumor and I’m ashamed that I bought into it. Nope! no wax, just weird chemical additives. Based on the brand you buy, here are the chemicals which may have been added to keep those morsels morsel-shaped during baking:

  • Soy lecithin: A common stabilizer in chocolate chips 
  • Ammonium phosphatides (AMP): An emulsifier used in chocolate to achieve the desired viscosity 
  • Glycerol monopalmitate (GMP): An emulsifier used in chocolate to achieve the desired viscosity 
  • Polyglycerol polyricinoleate (PGPR): A complement to emulsifiers that regulates the yield value in chocolate 

These stabilizers are why melting chocolate morsels for use in mirror coatings or in candy making creates a grainy mess that is thick and a little gloopy. Don’t do it.

Chocolate discs are also known as couveture chocolate, already tempered and designed to be melted. It is more expensive than morsels and will result in puddles of chocolate which spread out through your dough.

Baking chocolate? That’s where it’s at. This stuff is gold. Hand chopping results in tiny little bits which will melt completely and big ‘ol honkers which will give the cookie a great burst of chocolaty goodness. NOTE: if the chocolate is labeled as “candy,” don’t bake it. The results will disappoint you. And you know… die alone and whatnot.

Cookie Fact #14: Hand-Chopped Chocolate = Most Intense Flavor and Interesting Texture

So how do we pull these details together?

  • Chocolate chips produce the most regular cookies, with small, melty pockets of chocolate. 
  • Chocolate discs and chunks will cause some degree of layering in the dough, creating a flakier cookie with larger sections of molten chocolate.
  • Chopped chocolate produces the most contrast—the small bits of debris and chocolate shavings get dispersed throughout the cookie dough, disrupting its texture and giving a nice chocolatey flavor to the whole affair, while larger chunks still melt into large gooey pockets. The only way to get this effect is to hand-chop whole chocolate bars with a knife. Hand chopping also gives you control over the exact size of your chocolate chunks. Many people prefer a LOT of chocolate chopped into LARGE 1/2- to 1/4-inch chunks.

Cookie Fact #15: Warm Dough Alters Chocolate Dispersal

Properly tempered chocolate (if you’re a chocolate nerd, I’m talking chocolate with type V crystals) will melt at a relatively high temperature—around 95°F (35°C) or so. This is your callets and chopped chocolate bars.

By incorporating this kind of chocolate into dough that’s been allowed to rest in a warm spot until it gets above 95°F (near a preheating oven works), or by gently stirring already-made cookie dough that’s been warmed to above 95°F, you end up dispersing some melted chocolate throughout the dough.

The result is a sort of swirl effect that can be quite delicious if you do it carefully, though you miss out on the classic large melty pockets. If this seems overly finicky, it is! I don’t do this and don’t really recommend it. But if you want to experiment, try making you next batch of cookies made with dough that has been warmed to 80°F (27°C) and gently swirled. This melts the very tiniest bits of chocolate, but leaves the larger chunks intact.

And for God’s sake, don’t overwork your dough while adding in the chocolate! We’re not making crackers!

Perfecting Chocolate Chip Cookie Flavor

Ok, we’ve been at this for a while. Time for a quick recap. So far we’ve covered butter, sugar, eggs, leavening, flour, and chocolate. As far as covering the major chemical and physical players in the cookies’ final outcome, we’re done.

Here’s what we’re working with so far: White sugar is beaten into whole eggs until it dissolves. Butter is browned and chilled before being beaten into the egg mixture, along with brown sugar. Flour and baking soda are folded in very gently, along with chocolate.

Cookie Fact #16: Cookies Need More Salt Than You Think

Salt (and quite a bit of it) is essential to balance the flavor of caramelized sugars. Even with regular salt mixed into the dough, a popular addition is a little sprinkle of coarse sea salt to the tops of the cookies, gently pressing it in right as they come out of the oven for little crunchy bursts of salt that pop with each bite.

Cookie Fact #17: Inexpensive Vanilla is Indistinguishable From Fancy

A good amount of vanilla is a must (though, as our taste test has shown, even imitation vanilla flavoring will do just fine).

With flavor and ratios out of the way, it’s time to talk thermodynamics.

Pay Attention to Temperature

We’ve already seen how the temperature of the dough can affect how chocolate is incorporated, but it can also affect how it bakes. Both the starting temperature of the dough and the oven temperature have an impact.

Cookie Fact #18: Cooler Oven = Wide Cookies. Hotter Oven = Compact Cookies

Food scientists have experimented baking cookies at various temperatures in 25°F increments, ranging from 250°F (121°C) up to 450°F (232°C). When baked at a lower temperature, the dough has more of a chance to spread out, leading to flatter, wider cookies. Conversely, cookies baked at higher temperatures spread less. Even a difference of as little as 50°F (28°C) makes a HUGE difference.

Moreover, the lower the oven temperature, the more evenly the cookie bakes, with less of a contrast between the edges and the center. In fact, when the oven temperature gets low enough (around 275°F (135°C) and below), you completely lose any contrast, producing a cookie that’s more or less homogenous across the board.

Cookie Fact #19: Warmer Dough = Wide Cookies, Cooler Dough = Compact Cookies

Beyond oven temperature, starting temperature of dough also affects the outcome.

As you can see, cookies baked straight from the fridge will stay a little more compact, while those that are allowed to warm will spread more. By adjusting the starting temperature of the cookie dough and the temperature of the oven, you can create a wide variety of textures and contrasts.

For these reasons, it is best to start with cookie dough right from the fridge – 40°F (4°C). Baking in a 325°F (160°C) oven until the edges are nice and toasty brown will leave you with a cookie that’s still plenty soft and chewy in the center.

Giving the Cookie Dough a Rest

Cookie Fact #20: An Overnight Rest Yields Superior Flavor

If there’s one single thing you can do improve the flavor of your cookies, it’s to let the dough rest. They bake up darker and more flavorful. That butterscotch note that was barely hinted at when you baked the dough right after mixing? It’ll blow you away with its intensity and complexity by the second day.

So how does it work? Harold McGee explains it in Keys to Good Cooking. Turns out that during the resting process, both flour proteins and starches break down a bit. How does this help improve flavor?

It helps to think of proteins and starches as large LEGO structures. During the process of browning, those large structure are broken down into smaller parts and individual pieces and subsequently rearranged. Sort of like destroying that LEGO castle so you can build a dozen spaceships. Now, both of these phases—the breaking down and the reconstruction—take time.

By resting the dough, you give the deconstruction phase a head start. It’s as if you left your LEGO castle sitting out over night and your annoying little sibling came by and smashed it all, King of Tokyo-style. With the pieces separated, building your spaceships is much faster.

It’s really the same thing, except instead of LEGOs, you’ve got proteins and flour. Instead of an annoying sibling, you’ve got enzymes. And instead of awesome spaceships, you get awesome cookies. How awesome? We’re talking, oh, a million puppies on the moon wearing superhero underpants under their little doggie spacesuits levels of awesome.

And while it’s tough to be patient, awesomeness is something worth waiting for.

Understand Cookie Science and You’ll Make better Cookies

When all is said and done, what have we changed about the classic recipe? Browning butter and then chilling it, a good long rest on the dough, dissolving half the sugar in the eggs before incorporating it…. All this produces a cookie that hits all the right notes. A deep, rich, butterscotch-and-toffee flavor; crisp edges; a soft, chewy center; an irregular crumb structure with a craggy top; and a mix of chocolate dispersed through the cookie in fine threads and big gooey pockets, all with a nice sweet-and-salty balance.

Are they the simplest cookies in the world? No way. Are they worth the extra time and effort? Many people certainly think so.

The beauty of understanding how ingredients interact with each other is that even if one person’s  definition of the “best” chocolate cookie isn’t in line with yours, if you’ve read this far, then you know what you need to do to adjust almost any cookie recipe to suit your own tastes. Like your cookies chewier? Substitute some of that all-purpose flour for bread flour. Want your cookies to rise up a little taller? Add a touch of baking powder or replace the yolk of one of those eggs with an extra white. You like your chocolate in distinct pockets? Use chocolate chips instead of hand-chopped. Want your cookies more flexible and chewy? Just replace some sugar with a touch of corn syrup.

You get the idea. Doesn’t that make you feel all empowered and stuff?