Paleo Chocolate Muffins {Gluten-Free, Grain-Free, Dairy-Free, No Refined Sugar}
Published
Grain-free never tasted better! These easy and super moist Paleo chocolate muffins will satisfy your chocolate cake cravings. Made with simple and healthy ingredients. Gluten-free, dairy-free, grain-free and no refined sugar.

Paleo and grain-free baking.
I have been doing a lot of grain-free baking because my husband and I have been eating more Paleo to help with his migraines and autoimmune inflammation and my thyroid and adrenal issues.
Paleo simply means gluten-free, grain-free, dairy-free and no refined sugar.
Paleo muffins are a favorite of my family. I have been baking a lot of Paleo muffins in a variety of flavor combinations because they are my husband’s go to for breakfast, snacks, and dessert.
Seriously, I am baking Paleo muffins every other day. My husband and my kids love them and eat them so quickly that they usually don’t last but one day.
I love how easy they are to make and that they are a healthier version of your traditional gluten-free muffin. They are made with simple and healthy ingredients like almond flour, no sugar added applesauce and honey.
If you are new to grain-free baking, there are a few differences to traditional gluten-free baking with rice flour. Paleo grain-free baking is different than gluten-free baking, especially the texture.
The texture of almond flour is much denser than baking with rice flour. Even though it’s different from your traditional gluten-free baking, it’s a tasty different.
These Paleo chocolate muffins are super easy to make. They are a one-bowl wonder that can be made in less than 40 minutes. They are moist and chocolatey.
I don’t feel guilty about eating more than just one of these healthy Paleo chocolate muffins. I hope you enjoy them as much as my family and I do.
Also, check out my other Paleo muffin recipes.
- Paleo Banana Blueberry Muffins {Gluten-Free, Grain-Free, Dairy-Free, No Refined Sugar}
- Paleo Carrot Cake Muffins
- Paleo Pumpkin Chocolate Chip Muffins
- Paleo Chocolate Chip Pecan Pie Muffins
Paleo Chocolate Muffins {Gluten-Free, Grain-Free, Dairy-Free, No Refined Sugar}

Ingredients
- 2 cups almond flour
- 1/2 cup cocoa powder
- 1/2 cup honey
- 2 eggs
- 1 cup unsweetened applesauce, I buy the snack sizes they are 1/2 cup servings and keep them in my pantry for baking.
- 1 teaspoon baking soda
- 1/2 teaspoon baking powder
- 1/4 teaspoon of salt
- 1/4 teaspoon cinnamon
- 1 teaspoon of pure vanilla extract
- 1/8 teaspoon pure almond extract
- gluten-free and dairy-free chocolate chips, optional
Instructions
- Preheat oven to 350 degrees.
- In a large bowl add the wet ingredients first (eggs, applesauce, pure vanilla extract, pure almond extract and honey) and stir tother until fully combined.
- Then add the dry ingredients (almond flour, baking soda, gluten-free baking powder, salt, cinnamon and cocoa powder). Mix until fully combined.
- Scoop batter into a lined muffin pan. The batter will be thick. (I like to use an ice cream scoop.)
- Bake for 23-26 minutes. Please watch your oven because all ovens are different.
- Remove and check centers with a toothpick to see if they are done.
- Add chocolate chips to the top of hot muffins (optional).
- Allow muffins to cool before serving.
- Store in an airtight container.
- Enjoy!
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.















This is one of my favorite recipes!
Fyi. You can substitute the applesauce with canned pumpkin. It doesn’t change the consistency or flavor at all!
I’m wondering if there’s another grain free flour I could use instead of the almond flour? Would garbanzo bean flour work? Or cassava flour? Or quinoa?
Also, has anyone had success with an egg alternative such as psyllium husk, chia, or flax?
Hi, Cassava flour is your best option if you want to swap out almond flour—it has a neutral flavor and behaves more like traditional flour, so it can give you a sturdier, less crumbly result. It’s not a perfect 1:1 swap though, since it absorbs more liquid, so you may need to slightly reduce the flour or increase the moisture in the recipe to keep the texture balanced. Garbanzo bean flour and quinoa flour aren’t great choices here—they tend to have strong or bitter flavors that don’t work well in sweet baked goods. As for egg replacements like flax, chia, or psyllium husk, those can sometimes help with binding, but we haven’t tested them in this recipe, and they may change the texture quite a bit.
I just made these chocolate muffins and they all were sunken in the middle. I checked doneness with toothpick & they are done; any comment as to why this happened? The batter tasted delicious as I licked the mixing bowl!
Hi Sharon, a few things could be the cause. Sometimes mixing the batter too much adds extra air, which makes them rise fast and then sink. If your oven runs hot, that can do the same. Even if a toothpick comes out clean, the muffins might not be fully set in the center—try gently pressing the top to check. Using a bit too much baking soda can also cause them to puff up too much and fall. And finally, cooling them too quickly can make them collapse. Next time, try mixing gently, double-checking your oven temp, and letting them cool slowly in the pan.
Thanks, Amy, for responding with your suggestions. I will try not mixing too much next time, as I used the exact amount of baking soda and have not had any issues with my oven temp in all my baking, including my sourdough bread making. I have to say that the chocolate muffins were done and taste amazing! The sunken middle had no effect on the taste!
My husband always says about my baking “it tastes ok, but why do you have to healthify everything?” I made these and packed one in his lunch box today and he texted me to say “those chocolate muffins are the best ones yet!” High praise indeed! I had to share. The chocolate chips I used were sweetened with stevia, and I used half honey half maple syrup because I ran out of honey.
New to paleo and the first time baking with Almond flour. I thought they tasted really good. I used half applesauce and half of an overripe banana. Sweetness was perfect. Thanks for the recipe!
Love the taste of these but I’ve made them twice and they sink in the middle every time…what am I doing wrong???
Hi Ange, we recommend getting an oven thermometer and checking your oven temperature. Did you know that ovens can vary by up to 50°F from the stated temperature on the dial?
Mama Know Gluten Free has done it again! Absolutely delicious! I could eat all if these in one day. Swapped honey for maple syrup since that is what I had, and I always measure chocolate chips with my heart. I plan on freezing some for a quick snack option. Thank you!
These are so delicious! My family absolutely loves them!! So moist and a deep chocolate flavor. Delicious with a cup of coffee. My daughter in law is GF and I am always looking for new recipes without gluten. My son is looking to cut back on processed sugar and this recipe covers it all. Definitely a recipe I will make again and again!!
They turned out perfect! Thank you!
These are so good! They taste just like chocolate muffins! These are very moist so if you keep them longer than a couple days I recommend freezing or they can mold quickly. Mine froze just fine: 30 seconds to heat up and they’re ready to eat. Thanks so much for the recipe!
I just made these. I added a splash of maple syrup and did not use the baking powder (to keep it truly paleo). I also replaced the vanilla and almond extract with a splash of amaretto. These muffins are FANTASTIC. They grew in the oven, were incredibly moist and fluffy. They are the perfect amount of chocolate and perfectly sweet for a muffin. I would recommend these even if you aren’t watching your gluten.