Healthy Chocolate Chip Muffins (Gluten-Free)

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The BEST Healthy Chocolate Chip Muffins Recipe (Gluten-Free & Paleo)! These muffins are SO easy to make and taste SO good you’d never guess they’re healthy!

Front view of a healthy chocolate chip muffin with six other chocolate chip muffins around it and some chocolate chips sprinkled on the table

When I was younger I had a serious weakness for Hostess mini chocolate chip muffins. In other words, I seriously loved them.

For many years, every Friday during summer swim season we would walk across the street to 711 after morning practice to get breakfast. And every Friday, my breakfast of choice was a Slurpee (always Pina Colada or Coke Flavored), and a bag of Hostess mini chocolate chip muffins.

Because I was a kid/teenager I had no idea what it meant to eat healthy (and I totally didn’t care). But now, as an adult, I’ve traded Slurpees for Green Smoothies, and I created this healthy chocolate chip muffin recipe that tastes just as yummy but is much more nutritious than it’s store-bought counterparts!

These Healthy Chocolate Chip Muffins are gluten-free, Paleo-friendly and can easily be made dairy-free! They’re mixed up in one bowl and come together from start to finish in 30 minutes! Plus they have the taste and texture of a bakery chocolate chip muffin!

Front view of a healthy chocolate chip muffin with a bite taken out of it, with three other chocolate chip muffins in the background

How do you make Chocolate Chip Muffins? 

Let’s start by discussing how to make this paleo chocolate chip muffin recipe!  It really is SO simple! It’s made in one bowl and comes together in a snap! Here are a few notes to ensure your muffin-making success!

Step 1: Mix together dry ingredients & set aside

The first step in making these gluten-free chocolate chip muffins is mixing the dry ingredients together and setting them aside to use later. ,

I often do this to avoid needing to clean and dry my measuring cups after measuring the wet ingredients (because you can’t measure flour in a vessel that just held almond butter)!

Alternatively, you can simply add all the dry ingredients to the wet ingredients individually (as shown in the video), if you want to make this recipe using only one bowl!Either way works great!

Step 2: Mix wet ingredients together

Next, mix together the wet ingredients. Start by melting the almond butter and butter together and stirring until smooth.

Doing this ensures that the other ingredients in this chocolate chip muffin recipe, which may be cold, (like applesauce or eggs), won’t cause the butter/almond butter to solidify again!

Add the rest of the wet ingredients and mix well! Then add the dry ingredients to the wet ingredients and then stir to combine. Once the mixture is smooth, add the chocolate chips and stir until they are evenly distributed.

Step 3: Fill a muffin pan with the chocolate chip muffin batter

Use a 1/4 cup measuring scoop to fill each well of a greased standard muffin pan about 3/4 of the way full. As you can see below, this particular batch only made 9 gluten-free chocolate chip muffins! I usually get 10 muffins out of this recipe, but I must’ve added a touch more batter to each well than I usually do this time around.

It’s important that the pan is well greased so the chocolate chip muffins are easy to remove! I use a nonstick spray, but you can also grease the wells with butter, coconut oil or shortening!

Step 4: Bake & Cool! 

Bake the chocolate chip muffins for 20-25 minutes. You will know they are done when the tops are golden brown and spring back when touched, and a cake tester inserted in the center comes out with only a few crumbs.

Let the healthy chocolate chip muffins cool in the muffin pan for 5-10 minutes. Carefully remove them and transfer to a wire cooling rack to cool the rest of the way (or eat them warm)!

two overhead photos, the top one shows a hand filling a muffin in with healthy chocolate chip muffin batter, the bottom shows two hands holding a muffin pan with baked chocolate chip muffins in it.

How do you store Chocolate Chip Muffins? 

These healthy chocolate chip muffins can be stored at room temperature for two-three days, or in the refrigerator for up to a week.

Can you freeze chocolate chip muffins? 

YES!! I make these and freeze them all the timeTo freeze:

  1. Let the muffins cool completely to room temperature.
  2. Transfer cooled muffins to an airtight container or plastic bag.
  3. Freeze!

To reheat: place frozen muffin in the microwave and heat for for 30-60 seconds per muffin!

Can you make Mini Chocolate Chip Muffins? 

Yes! You can make these into mini chocolate chip muffins using a mini muffin tin! You will need to adjust the bake time. I recommend checking them after 12 minutes but they could take up to 18 minutes to bake depending on your oven!

More delicious recipes!

If you love muffins as much as we do, here are some more healthy muffin recipes to try!

Front view of three healthy chocolate chip muffins

Healthy Chocolate Chip Muffins: Ingredients and substitutions

Let’s take a minute and chat about the ingredients used in this gluten-free chocolate chip muffin recipe, as well as possible substitutions! I must start by saying one thing…

Do not change the type/amount/ratio of flours in this recipe (I will explain more below)

  • Coconut FlourCoconut flour is a gluten-free baking pantry staple in my house. However, please listen carefully…you cannot make any substitutions for coconut flour. It is a very unique flour and absorbs significantly more liquid than other flours. If you try substituting the coconut flour your muffins will not turn out well! Don’t do it, ok?
  • Almond FlourI also do not recommend substituting the almond flour in this chocolate chip muffin recipe. Gluten-free/Paleo baking is a science and I tested this recipe extensively to ensure it was perfect.
  • Sugar. Any granulated sugar works well in this recipe. I usually bake with organic cane sugar (I buy it from Costco). To make these Paleo chocolate chip muffins, use coconut sugar!
  • Butter. Salted or unsalted butter works well in this paleo chocolate chip recipe (use grass-fed for Paleo baking). You can also substitute coconut oil or ghee for a dairy-free version!
  • Almond Butter. I’m guessing any nut or seed butter would work well in this recipe. I have only tried almond butter and cashew butter (YUM) and had great results with both.
  • Applesauce. To be sure there are no refined sugars in these chocolate chip muffins, use unsweetened applesauce!

Front view of nine healthy chocolate chip muffins on a cooling rack, the front center muffin has a bite taken out of it


Healthy Chocolate Chip Muffins (Gluten-Free & Paleo-Friendly)

The BEST Healthy Chocolate Chip Muffins Recipe (Gluten-Free & Paleo)! These muffins are SO easy to make and taste SO good you'd never guess they're healthy! 
5 from 2 votes
Course Breakfast, brunch, Snack
Cuisine American
Servings 10 muffins
Calories 177.9
Prep Time5 minutes
Cook Time20 minutes
Cooling time5 minutes
Total Time25 minutes



  • Preheat oven to 375 degrees F. Grease a 12-cup muffin tin, set aside.
  • In a small bowl combine coconut flour, almond flour, baking powder, baking soda, salt, cinnamon and sugar. Set aside.
  • In a large, glass mixing bowl melt together butter and almond butter (for about 1 minute on high), stir until combined.
  • Add applesauce, vanilla and eggs and stir until smooth.
  • Add dry ingredients to wet ingredients and mix until completely combined.
  • Gently fold in chocolate chips.
  • Pour about ¼ cup of batter into each muffin well (so it’s about ¾ of the way full).
  • Bake in preheated oven for 18-22 minutes or until the tops are set, golden brown, and a toothpick inserted in the center comes out with only a few crumbs.
  • Let cool in the pan for 5 minutes before gently removing each muffin from its well and transfer them to a wire rack to cool.
  • Enjoy!
  • To freeze: let cool then place muffins in an airtight container and put in the freezer. To reheat microwave on high for about 30 seconds per muffin!



Serving: 1muffin | Calories: 177.9kcal | Carbohydrates: 15.7g | Protein: 4.1g | Fat: 12.3g | Saturated Fat: 4.7g | Polyunsaturated Fat: 0.4g | Monounsaturated Fat: 1.6g | Cholesterol: 49.6mg | Sodium: 156mg | Potassium: 57.6mg | Fiber: 3g | Sugar: 4.7g | Vitamin A: 205IU | Vitamin C: 0.2mg | Calcium: 27mg | Iron: 0.8mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Did you enjoy this recipe? Have a question? Leave a comment below!

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  1. I mean, if we are being honest here, I am a complete sucker for chocolate chip muffins. They are by far my favorite but I don’t ever feel like it’s ok to make them when I can make blueberry or raspberry muffins instead. But hey! Laura does it again with her healthier recipe and I don’t feel alllll the guilt when I make these for my family. And, they are so simple, so tasty – there’s really no reason to atleast give them a try! Guilt free over here and devouring these any chance I get. They are SO good!!

  2. I really wish I had coconut flour now, because these look perfect. 🙂 I love how you were very specific about not making substitutions.