These fluffy, decadent Gluten Free Chocolate Chip Muffins are perfection made with almond flour. Gluten free flour blends often yield crumbly or dry baked goods. These are the perfect texture and are always a hit with my son!

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Gluten Free Perfection!
A few years ago, I had to put my pizza and pasta-loving son on a gluten and dairy free diet. It was a difficult transition for a very picky eater.
I developed this almond flour chocolate chip muffin recipe to help us get through the transition. I wanted to make something that appealed to him (chocolate chips!), but was gluten and grain free (almond flour!), and had protein and healthy fats to make it satiating (eggs and coconut oil!).
These nutritious, but still fun, gluten free chocolate chip muffins were a lifesaver. He loved having them packed in his school lunches, and his friends at school loved them and starting asking him to have his mom pack two so he could share.
I skip gluten-free flour blends that are full of starches and gums. Not only are they void of nutrition, they also create dry and crumbly baked goods. Almond flour is a pretty magical option! It’s lightly sweet, looks and tastes like regular baked goods, and is lower in carbs and higher in healthy fats and proteins.
Why You’ll LOVE these Gluten-Free Chocolate Chip Muffins
- Wholesome, simple ingredients! No weird gluten-free baking flour, no xanthan gum, no white sugar, no seed oils. These pantry staples are easy to have on hand.
- Kid-Friendly, Mom Approved! Often “healthier” baking doesn’t appeal to picky eaters. These healthy chocolate chip muffins are a lifesaver with little ones.
- Freezer Friendly. We keep a batch of these in the freezer for quick snacks or to add to meals to make them more fun. My son loves eating them while they are still frozen!
- One Bowl, less mess! No need to mix your dry ingredients and wet ingredients in two separate bowls. This recipe reduces clean up! It’s an easy recipe even kids can master.
- They are perfect for anyone with food intolerances or celiac! Almond flour and arrowroot are grain-free and safe gluten-free ingredients.
What You’ll Need
- Almond Flour
- Arrowroot (can sub tapioca or organic corn starch)
- Baking Soda
- Baking Powder
- Sea Salt
- Eggs
- Coconut Oil (avocado oil or a light tasting olive oil are great options as well. Melted butter also works as a sub.)
- Maple Syrup (honey or date syrup work!)
- Vanilla Extract
- Chocolate Chips (we love dark chocolate chips!)
Kitchen Tools
- Parchment Paper Liners prevent gluten-free muffins from sticking!

How to Make Gluten Free Chocolate Chip Muffins
Step 1: Preheat oven to 350º F. Line a standard muffin pan with 12 muffin liners. Set aside.
Step 2: In a large mixing bowl, combine maple syrup, coconut oil, eggs, and vanilla. Whisk to combine.


Step 3: Into the bowl, add the arrowroot, baking powder, baking soda, and sea salt. Mix until incorporated into the wet ingredients.
Step 4: Add the almond flour into the mixture, and stir until just combined.


Step 5: Fold the chocolate chips into the muffin batter with a silicone spatula.
Step 6: Divide the muffin batter equally between 12 muffin liners. The muffin batter should almond fill the liners. Sprinkle a few extra chocolate chips on the top of each muffin.


Step 7: Bake muffins for 18-20 minutes, until the centers are fully cooked the muffins have golden tops. Be careful not to overcook almond flour muffins – almond flour goes from golden to burned much more quickly than wheat flour!
Step 8: Leave the baked muffins in the muffin tin to fully cool prior to removing them.


How to Store Leftover Muffins
Once the muffins have fully cooled to room temperature, put the muffin pan with the muffins in the freezer for at least 15 minutes to solidify the chocolate chips. Then remove the muffins from the muffin tin and store them in an airtight container or ziplock freezer bag.
The muffins stay fresh when frozen and can be frozen for up to 6 months. The muffins are delicious straight out of the freezer while still frozen!
Variations:
Make fun bakery-style muffins: As an occasional treat, we make these in a jumbo muffin pan. This recipe will make 6 extra large muffins.
Mini Muffins: Make this recipe in a mini-muffin pan for adorable treats, perfect for adding to a big breakfast spread or for little ones to snack on.
Add Nuts or Berries: Raspberries, blueberries, walnuts or pecans are great additions to these fun chocolate chip muffin recipes. Add 1 cup of fresh berries or 1/2 cup of chopped nuts to the the batter when folding in the chocolate chips and bake the same as directed in the original recipe.
Add a Twist: Add white chocolate chip, mini chocolate chips, milk chocolate chips, or peanut butter chips for a twist to keep them from getting boring!
Gluten-Free Muffins: Make this recipe without the chocolate chips for a basic vanilla muffin! Or add berries and make gluten-free blueberry muffins or gluten-free raspberry muffins.
Gluten-Free Chocolate Chip Bread: Make this recipe in a loaf pan for a chocolate chip quick bread. Prepare the batter as directed and add the batter to a parchment paper-lined standard loaf pan. Bake the bread for 20 minutes at 350º F, then add foil to the top to prevent over browning. Continue to bake the chocolate chip loaf for 25-30 minutes, until set in the center.
Gluten-Free Banana Muffins: Try these Healthy Banana Muffins made with oat bran and almond flour!
Other Gluten Free Almond Flour Recipes
- Almond Flour Pancakes
- Fudgy Almond Flour Brownies
- Paleo Chocolate Chip Cookies
- Gluten-Free Double Chocolate Muffins (made with almond flour and oat flour)
I’d love to connect with you on social media! Find me on Facebook or Instagram where I post daily healthy eating and lifestyle inspiration!

Gluten Free Chocolate Chip Muffins
Equipment
- muffin tin
- parchment paper liners https://amzn.to/4jUT5UH
Ingredients
- 4 eggs preferably pastured eggs
- 1/2 cup maple syrup
- 1/3 cup coconut oil
- 2 teaspoons vanilla extract
- 1/4 cup arrowroot *sub organic corn starch or tapioca flour
- 2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1/4 teaspoon sea salt
- 2 1/2 cups almond flour
- 1/2-1 cup dark chocolate chips 70% or higher recommended
Instructions
- Preheat oven to 350º F. Line a standard muffin pan with 12 muffin liners. Set aside.
- In a large mixing bowl, combine maple syrup, coconut oil, eggs, and vanilla. Whisk to combine.
- Into the bowl, add the arrowroot, baking powder, baking soda, and sea salt. Mix until incorporated into the wet ingredients.
- Add the almond flour into the mixture, and stir until just combined.
- Fold the chocolate chips into the muffin batter with a silicone spatula.
- Divide the muffin batter equally between 12 muffin liners. The muffin batter should almond fill the liners. Sprinkle a few extra chocolate chips on the top of each muffin.
- Bake muffins for 18-20 minutes, until the centers are fully cooked the muffins have golden tops. Be careful not to overcook almond flour muffins – almond flour goes from golden to burned much more quickly than wheat flour!
- Leave the baked muffins in the muffin tin to fully cool prior to removing them.
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