Paleo Chocolate Muffin (grain-free, gluten-free)

This Paleo Chocolate Muffin is grain-free, gluten-free, and dairy-free, and SO delicious! All you need is one bowl and 30 minutes, and you can enjoy these decadent paleo protein muffins.

In the Crowded Table house, we love snacks! My kiddos are always asking me for a snack and sometimes it’s hard to keep up. We do easy ones like fruit or nuts, but sometimes a homemade snack hits the spot. I make a ton of muffins for quick breakfasts and snacks, so I wanted to mix it up a little bit and try a paleo chocolate muffin. These muffins have just a hint of cinnamon, and are perfect for an easy paleo breakfast muffin or grab and go snack. I love that they have protein and healthy fat hidden in there as well!

How to make these Paleo Protein Muffins:

  • Mix all the ingredients together in one bowl
  • Pour into muffin tin and bake
  • Enjoy!

Tips for Making these Paleo Chocolate Muffins:

  • You can substitute maple syrup for the honey, just add 2 teaspoons coconut flour to help absorb the extra moisture
  • If your almond butter is super liquidy, drain off some of the oil. It should be thick and creamy
  • Use about 1 1/2 cups of cubed butternut squash to make the puree – just steam it and puree it in a food processor or blender. Or used canned butternut squash puree or pumpkin puree.
  • This recipe also makes for a great paleo chocolate cupcake – just add frosting!
  • For paleo chocolate, I love THIS brand 🙂

Is all dark chocolate paleo?

This question comes up alot, so I wanted to be sure to address it. All dark chocolate is NOT paleo, usually because some refined sugar is added, or sometimes a refined oil is used as well. The best way to tell is to look at the label – if all the ingredients are paleo friendly (like this brand), then you’re good to go! However, if cane sugar is listed, or any other refined sugar, then it is not officially a paleo approved chocolate.

Paleo Chocolate Muffins

  • Author: 
  •  Prep Time: 10 min
  •  Cook Time: 20 min
  •  Total Time: 30 minutes
  •  Yield: 18 muffins 1x
  •  Category: Breakfast
  •  Cuisine: American


These Paleo Chocolate Muffins are paleo, gluten free, and dairy free, and SO delicious! All you need is one bowl and 30 minutes, and you can enjoy these decadent muffins.



1 cup almond butter

1 cup butternut squash puree (or pumpkin puree)

1 cup apple sauce

2 eggs

1/2 cup honey

2 teaspoons vanilla extract

1/2 cup cocoa powder

1/4 cup flax meal

1 teaspoon cinnamon

1 teaspoon baking soda

1/4 teaspoon salt

1/2 cup dark chocolate chips (paleo friendly)


Preheat oven to 375 degrees F.  Grease or line 18 muffin cups.  Mix all ingredients in a large mixing bowl until well combined.  Scoop 1/4 cup batter into each muffin cup.  Bake for 18-22 minutes, rotating pan halfway through baking (after about 10 minutes).  Allow to cool completely before removing from muffin tin.  Enjoy!