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If there’s one thing I’ve learned after all of these years in recipe development and baking for others, it’s that people are particular about their cookies. Like, really particular. You have the chewy, crisp, soft, pillowy, crunchy edges, warm, cold, frozen, room temperature, perfect-for-the-first-too-soft-the-second... it’s an opinion that’s often expressed the second they take a bite.

When I was young, I was all about the soft, cakey cookies. Then somewhere in my twenties, I graduated to crisp edges with a chewy center. Later, I went for a solid crunch. And now, it changes all the time. (Heck, let’s be honest: I just want the cookie).

As I’ve been working through my baking science posts, focusing on revamping favourites and making modifications, I figured it was pretty essential to know how to perfect your chocolate chip cookie. Understanding the roles of each of the ingredients will help you achieve success, especially when it comes to remaking your old favourites with an allergy-friendly twist.

There are already some great resources out there for cookie chemistry basics. This TedED animation on cookie science, Serious Eats’ super detailed post on The Science of the Best Chocolate Chip Cookies, and Handle the Heat’s ultimate guide are some essentials to read.

Baking perfection does require some diligence and attention to detail, especially when you’re revamping a recipe or creating it from scratch. I could go on and on about this (and I usually do: you can ask me your questions on my Facebook page), but for now, here’s a simplified version to understand the role of allergy-friendly substitutions and making the cookie you crave.

The Ingredient: Butter

Chocolate chip cookies most frequently call for butter, which, of course, contains dairy. Replacing it with margarine (even most dairy-free versions) doesn’t always deliver the same result: many brands contain too high of a water content, which is designed to keep it spreadable straight from the fridge, not for baking perfection. An exception to this is Earth Balance, whose water content is on par with butter.

Oil and shortening—which are dairy-free—change the texture of the cookie, often making it soft or cakey. While you can substitute (a rule of thumb is 1/2 cup butter = 6 tablespoons oil), I really recommend sticking to a buttery spread for that taste and texture you remember.


  • Firm fat will take a longer time to melt, resulting in cookies that hold their shape
  • Melted then chilled fat is best for thick and chewy cookies

The Ingredient: Eggs

Like butter, eggs are often used in conventional baking, and each part of the egg—the yolk and the white—have their own role. Egg whites are higher in protein and add structure, but can also be sticky or wet (think meringues). Yolks contain the fat, providing binding power, flavor, and tenderness. If the recipe calls for eggs (which most do, other than shortbread), think of what you want the end result to taste like and go from there.

If you want:

  • Crunchy cookies: swap 2 tablespoons water per egg
  • Chewy cookies: use 2 tablespoons water + 1 tablespoon ground flaxseed per egg
  • Soft cookies: use 2 tablespoons applesauce per egg
  • Cakey cookies: add 1/4 teaspoon baking powder to the recipe

The Ingredient: Sugar

Sugar is (thank goodness!) allergy-friendly, but if its texture you’re after, the type of sugar you choose matters. Sugar not only adds sweetness but also binds to water in baking. This means the amount is important – too much sugar equals a crumbly cookie, and too little makes it tough. When it’s baked, it firms up, which is what delivers that crispiness.

Common options:

  • Brown sugar: has a higher water content and contains molasses; the more you use, the less it will evaporate in the cookie – resulting in one that’s a little softer
  • Granulated white sugar: less water plus no molasses equals a crisper cookie
  • Liquid sugar (maple syrup, agave nectar): adds softness and a bit of chew
  • Confectioners’ sugar: contains cornstarch and firms up the cookie

The Ingredient: Flour

Then there’s the flour... that whole “gluten” thing. Most run-of-the-mill cookie recipes call for all-purpose flour, which is what creates the actual dough. The starch in the flour absorbs the other ingredients, and the proteins bind to bring it all together. When it’s baked, everything is trapped into a cohesive disc of delicious, expands slightly, and becomes tender. Too much flour results in a crumbly cookie; too little contains too much water and will spread far too thin.

Making it simple:

  • Solo gluten-free flours contain little to no protein, which makes too crumbly (brown rice flour) or too chewy (tapioca flour); they also have disproportionate amounts of protein and starch and strong flavors (quinoa flour)
  • Gluten free, all-purpose flour is a one-stop shop, with balanced amounts of protein and starch, along with additional protein and inulin for structure and stability.
  • Adding xanthan gum to the recipe balances out the binding and emulsifies the ingredients for a smooth texture.

The Other Ingredients

Baking soda and baking powder, salt, and other ingredients also can influence what happens to your cookie (and other baked goods). Ratios of all of these, and the other, ingredients are important, too. But for now, these basics will get you started in creating your ultimate cookie.

I’ve created 3 amazing allergy-friendly chocolate chip cookie recipes, fit for all consistency requests: (1) thick, crisp and chewy, (2) thin and crunchy, and (3) soft and cakey. Read more below!

Thick, Crisp, and Chewy Chocolate Chip Cookies

The thick, crisp, and chewy chocolate chip cookies are usually the ones people request. These are the firm-on-the-edges, slightly chewy, thick, and a bit soft. The texture comes from the flaxseeds (which add density and moisture), along with the ratio of ingredients. The chilling time enhances the flavor and solidifies the fat, which helps with the chewiness. Pro tip: using Dark Chocolate Morsels is a great way to complement the richer flavor of this batch.

Thin and Crunchy (or Chewy) Chocolate Chip Cookies 

Thin cookies can be crunchy or chewy, depending on how long you bake them. They have a high fat ratio, which helps them spread and gives a really buttery flavor. No “egg replacer” is needed here; just some extra water does the job. Because they are so thin, keep your eye on the baking time; even an extra minute will change them from chewy to crunchy to burnt. Pro tip: use Mini Chips to coincide with the minimal height of the cookies.

Soft and Cakey Chocolate Chip Cookies

Melt in your mouth and super soft, these have a lower fat and higher flour content, and not as much sweetness as the others. The baking powder gives them a little more lift, and the chilling time helps them keep their shape. Pro tip: use Mega Chunks since they can make their way throughout the roomy dough.

My advice: make all 3 recipes! Prepare and bake in order, for the best timing on getting fresh cookies out of the oven and putting in the next batch.

About Laurie Sadowski
Laurie Sadowski is the author of three cookbooks devoted to gluten-free, vegan, and allergy-friendly baking. Using baking chemistry as a basis, everything is developed—and guaranteed—to taste ‘just like the real thing’. For more, visit