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Almond Flour Chocolate Chip Muffins are easy to toss together at a moment’s notice, and make for a high protein treat! If you’re a big fan of chocolate chip cookies, you may just love this muffin version!

Plate of chocolate chip muffins with one sliced in half so you can see the inside.

For my fellow muffin lovers who think chocolate chip cookies are the superior dessert of the universe, these healthier high protein Almond Flour Chocolate Chip Muffins are for you!

Not only are they infused with amazing flavor and feel like an absolute treat, but they are also made with wholesome ingredients like almond flour, cottage cheese, eggs, and a touch of pure maple syrup.

So we’re sending pleasure signals to our taste buds while getting a dose of nutrition too.

These high protein muffins make an excellent treat while honoring your daily protein intake goal. Plus, they taste so lovely that even those who aren’t looking to track protein will find them scintillating as well.

Ingredients for Almond Flour Chocolate Chip Muffins:

Almond Flour: Taking the place of all-purpose flour, almond flour yields a light and fluffy texture and also brings a decent amount of protein to the muffins.

It also contributes healthy fats and some fiber, making it an ideal replacement for regular flour for those who are gluten intolerant or simply love baking with minimally processed foods.

Tapioca Flour or Gluten-Free All-Purpose Flour: Because almond flour doesn’t contain starch, almond flour recipes are benefitted by the addition of starch. I add tapioca flour or gluten-free all-purpose flour to yield a texture that closely resembles regular all-purpose flour.

Eggs: A few eggs help the batter rise substantially to make the loveliest fluffy texture. I don’t recommend using an egg substitution in almond flour recipes, as I find they tend to turn out very dense with a raw-like consistency in the center.

Cottage Cheese or Greek Yogurt: Here for moisture and protein, cottage cheese or Greek yogurt further ups the ante on our protein count.

Avocado Oil: For the best results, we need a little extra fat in the form of oil to make the muffins taste rich and moist. You can replace it with olive oil or melted coconut oil.

Pure Maple Syrup: The natural sweetener here, a little pure maple syrup is all we need since most of the sweetness comes from the chocolate chips. Honey or agave nectar works too.

Pure Vanilla Extract: A splash of vanilla adds a warm nuance to the flavor profile.

Chocolate Chips: Pick your favorite kind of chocolate chips. I use semi-sweet chocolate chips but dark chocolate chips, milk chocolate chips, and sugar-free chocolate chips work great too.

Baking Powder: The leavening agent here. Baking powder helps the batter rise to maximum fluffiness.

Ground Cinnamon: Here for a little extra flavor! I love the combination of cinnamon and chocolate and add cinnamon to most of my baked goods. Skip it if you aren’t into it.

Sea Salt: A pinch of salt enhances the flavors for the absolute best tasting result. Don’t skip it!

Ways to Customize:

Dairy-Free Option: Use ½ cup of avocado oil and omit the cottage cheese. This substitution will make them paleo muffins.
Make it Oil-Free: Omit the oil and use ⅔ cup of cottage cheese. The muffins won’t turn out as moist and rich, but they will still taste great.
Almond Flour Only: Omit the tapioca flour and add another ⅔ cup of almond flour if you prefer sticking with just almond flour.
Make it Fruity: Swap out the chocolate chips for fresh blueberries, chopped strawberries, raspberries, chopped cherries, apple, etc.

How to Make Almond Flour Chocolate Chip Muffins:

Preheat the oven to 350 degrees Fahrenheit and line a muffin pan with paper liners.

In a large bowl, mix together the eggs, cottage cheese, avocado oil, pure maple syrup, and pure vanilla extract until the wet ingredients are well combined.

Cottage cheese, eggs, pure maple syrup, and oil in a mixing bowl to make muffins.

Mix together the almond flour, tapioca flour, baking powder, cinnamon, and sea salt in a separate bowl to combine the dry ingredients.

Almond flour, tapioca flour, ground cinnamon, and baking powder in a mixing bowl to be stirred together.

Add the dry ingredients to the bowl with the wet ingredients and mix until a smooth batter forms.

Dry ingredients on top of wet ingredients in a large mixing bowl.

Stir in the chocolate chips.

Bread batter in a mixing bowl with chocolate chips added in.

Transfer the muffin batter to the prepared muffin tin, filling the holes ⅔ to all the way up. I like making larger muffins, so I fill the muffin holes up all the way and make 9 large muffins.

Muffin pan with raw muffin batter inside to be baked.

Bake on the center rack of the preheated oven for 20-25 minutes, or until the muffins test clean. Insert a digital thermometer in the center of one of the muffins. They are ready if the internal temperature is 190 degrees F or higher.

Muffin tray with chocolate chip muffins and chocolate chips in a bowl in the background.

Remove the muffins from the oven and place them on a cooling rack (I use my stove top) to cool completely. Allow the muffins to cool to room temperature before peeling off the paper liners to enjoy one.

If the muffins are still warm when you peel off the liner, you’ll lose some of the muffin to the liner.

Enjoy one warm with a little melted butter, peanut butter, or almond butter spread on top.

Storage Options:

Room Temperature: Store muffins in an airtight container or a large zip lock bag on the counter for up to 2 days.
Refrigerator: Refrigerate muffins for up to 5 days.
Freezer: For longer term storage, transfer muffins to a freezer bag and freeze for up to 2 months.

Plate of chocolate chip muffins with a smaller wooden plate with a single muffin in the background and a bowl of chocolate chips.

The next time you’re looking for a treat that is both sultry and wholesome, whip up a batch of these healthy chocolate chip muffins! It makes for an easy breakfast using healthy foods and no refined sugars. A treat you can feel good about!

I have a sneaking suspicion the whole family will love them.

If you’re a big fan of baking almond flour muffin recipes, try some of my other favorite muffin recipes.