Grain-Free Paleo Chocolate Chip Pumpkin Muffins made with coconut flour and naturally sweetened with honey or pure maple syrup.

Paleo Chocolate Chip Muffins - grain-free, dairy-free, refined sugar-free, and healthy!

Do you all remember the Muffin Top Movement circa 2003ish, during which muffin tops were the thing?

No one cared about the muffin bottoms, and you could even buy a muffin top pan so you could cut to the chase and save yourself the headache of the dreadful muffin bottoms?


I’m going to go ahead and say we had it all wrong.

Muffin bottoms are where it’s at.

Muffin stems, if you will

Particularly true with these muffins. Especially true with these muffins.

Probably because all the chocolate chips congregate in the midsection (upper stem if you will) of the muff, creating a pocket of melty dark chocolate goo surrounded by pumpkin spice fluff.

It’s kind of like your taste buds are touring the lost city of Atlantis on an airboat manned by talking spider monkeys on a river populated by finned unicorns with Channing Tatum as your tour guide and Elton John featuring Eric Clapton playing in the background. It’s.just.that.stimulating.

What were we talking about?

Ah yes, muffin bottoms. And how they’re dope.

As you can imagine, the recipe development portion of this venture was a real hoot.

It involved what I affectionately refer to as the No Batter Left Behind Act, a rubber spatula, and my face. I think you know where I’m going with this.

It also involved no less than 36 muffins (because: recipe testing), and my face some more. And when I say, “36 muffins,” I should clarify that the bottom portion of 18 of said muffins magically disappeared mere seconds after the muffins saw the light of day, because as previously stated, the bottoms are devilish little tempters, and as also previously stated: recipe testing…via my face. Make sense? Muffin top, anyone? I’ve got 18 to spare.

Anyhoo, you make these muffins in a blender.

Shocked? I know, it’s just the darndest. But don’t put the chocolate chips in the blender with all the ingredients lest you end up with flecked muffins versus studly studs of chocolate goo. The stud muffins are what we’re shooting for. Buh dum ching.

Grain-Free Chocolate Chip Pumpkin Muffins made with coconut flour and sweetened with honey (or pure maple syrup) - healthy enough to eat for breakfast! #muffin #recipe #almostpaleo #glutenfree

Ingredients for Grain-Free Pumpkin Muffins:

  • I made these grain-free using coconut flour…
  • refined sugar-free using honey…
  • dairy-free using almond milk…
  • stoked them out with fresh ginger…
  • dark chocolate chips, don’t panic!

Grain-Free Chocolate Chip Pumpkin Muffins made with coconut flour and sweetened with honey (or pure maple syrup) - healthy enough to eat for breakfast! #muffin #recipe #almostpaleo #glutenfree

A side note about muffin cups – Now, I wouldn’t consider myself to be a baker by trade, but what I noticed with these muffins was the foil cups worked better than the paper ones.

The muffins stuck a little to the paper cups, which didn’t stop me from scraping the papers clean, but for easier access to the muff, I would recommend using the foil cups.

In the words of Tay Sway, don’t say I didn’t say I didn’t warn ya.

Paleo Chocolate Chip Pumpkin Muffins – blowing muffin tops out of the water since 2015.

Grain-Free Chocolate Chip Pumpkin Muffins made with coconut flour and sweetened with honey (or pure maple syrup) - healthy enough to eat for breakfast! #muffin #recipe #almostpaleo #glutenfree

Grain-Free Chocolate Chip Pumpkin Muffins

5 from 1 vote
Grain-Free Chocolate Chip Pumpkin Muffins are a fall infusion of deliciousness for breakfast or snack!
Prep Time 15 minutes
Cook Time 45 minutes
Total Time 1 hour
Servings: 12 Muffins



  • Preheat the oven to 375 degrees F and line a 12-hole muffin tray with foil liners.
  • Add all of the ingredients except for the chocolate chips to a blender or food processor. Blend until completely smooth. Stir in the chocolate chips.
  • Scoop pumpkin muffin batter into the lined muffin tray, filling the holes ¾ of the way up.
  • Bake on the center rack for 40 to 50 minutes, or until muffins are golden-brown around the edges and have set up.
  • Allow muffins to cool for at least 30 minutes before unwrapping and devouring them.


Serving: 1Muffin · Calories: 204kcal · Carbohydrates: 24g · Protein: 4g · Fat: 11g · Fiber: 3g · Sugar: 13g
Author: Julia
Course: Breads
Cuisine: American
Keyword: chocolate chip pumpkin muffins, grain-free pumpkin muffins, paleo pumpkin muffins
Did You Make This Recipe?I want to see it! Tag @the.roasted.root on social media!

More Healthy Pumpkin Treats:

Paleo Pumpkin Pie

Paleo Pumpkin Pie - refined sugar free, dairy free, gluten free, and healthy! | #dessert #pumpkin #recipe #healthy

Maple Pumpkin Cheesecake Bars

Maple Pumpkin Cheesecake Bars | gluten free and naturally sweetened

Flourless Pumpkin Bars

Grain Free Almond Butter Pumpkin Bars #glutenfree @barneybutter

Julia Mueller
Meet the Author

Julia Mueller

Julia Mueller is a recipe developer, cookbook author, and founder of The Roasted Root. She has authored three bestselling cookbooks, – Paleo Power Powers, Delicious Probiotic Drinks, and The Quintessential Kale Cookbook. Her recipes have been featured in several national publications such as BuzzFeed, Self, Tasty, Country Living,, etc.

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Questions and Reviews

  1. i like that these are heavily studded with chocolate chips! now those are my kind of muffins 🙂

  2. I SO agree! You need that bottom of the muffin to spread stuff on, right?! Also, gimmie all those pickets of melty dark chocolate, BEST part.

  3. All I can think about when I see the words muffin top is the rim of fat above my jeans, lol! It’s my problem area. 😉

    But I agree, the bottom is where it’s and these are the sexiest muffin bottoms on the block. I love that they’re made in a blender too. That’s my new favorite way to make muffins- makes life so easy!

  4. YES! The bottom of the muffin is just as important and delicious as the top! These look fan-freaking-tastic m’dear! Pinning!

  5. Looks amazing! Can the tapioca flour be replaced with anything (ideally also something healthy-ish, like rice flour, corn flour, polenta, …)?

    1. Hi Sunni! I haven’t tested this recipe using tapioca flour replacements, but I believe you can replace it with with 1/3 cup of corn starch, potato starch, or arrowroot flour. This is me guessing based on previous experience, so I hope it works out! Let me know if ou try the recipe with any of those options!

  6. haha oh gosh yes, I definitely remember the muffin top fad! Too funny.

    These muffins sound fantastic – I have a bunch of leftover pumpkin right now that I must put to use with some of these!

  7. YES to pumpkin chip muffins! We are twinning in our GF pumpkin obsession here 🙂 And the congregation of chocolate in the center sounds d i v i n e 🙂 Pinning!!

  8. Okay, I have to admit, I am the ULTIMATE muffin top hoarder. I have a bad reputation among my friends for stealing muffin tops during gatherings. But those muffin stems (or stumps, as I usually call them) look positively delicious. LOVE all those chocolate chips in there!

  9. Goodness, these look good! Clearly pumpkin is on everyone’s brain this week. I just made pumpkin muffins too!

  10. Muffin stems! Haha! I love that! I do love my muffin tops but you are so right about the muffin stems, they got all the good stuff in them! I could live on pumpkin muffins this time of year and these look delicious 🙂

  11. I’ve been craving something sweet with pumpkin recently (as with most other people on the internet!) and this look absolutely perfect. This whole post nearly made me squeal with pumpkin excitement at how delicious everything looks!

    Issie x

  12. “½ + cup 2 tablespoons coconut flour”
    Can you clarify the above measurement for the coconut flour
    Is it 1/2 plus one cup plus 2 Tablespoons, or 1/2 cup plus 2 tablespoons?


  13. I made these muffins twice and both times they came out of the oven crisp on the outside and almost raw on the inside (most likely due to the number of eggs). Both times I “estimated” the coconut flour because the amount listed in the recipe doesn’t make sense. The second time I made them I also revised the recipe using less soy and a little extra tapioca flour to create a less watery batter but to no avail. Either I’m doing something wrong, or there’s something wrong with the recipe. Very disappointed because they looked delicious.

  14. Eva’s right. These are raw in the middle as crisp on the outside. I don’t see how the rawness could come from the eggs. We are cooking for a sufficient amount of time/heat and I’ve made other, coconut flour paleo muffins that came out fine. There is just too much moisture in these muffins! Too bad the recipe doesn’t seem to work because the flavor of the muffins is delicious.

  15. Julia, I think you are a genius, a wonderfully creative cook/baker, etc. I love all you do & say. Thank you so much. You are a breath of fresh air in this stale old universe, bahahaha. Take care…