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These Healthy Chocolate Muffins taste like a brownie, with a sneaky veggie hidden inside. There’s no flour or oil required, so they are naturally gluten-free, and kids love them!

chocolate muffins in pan and on a plate.

This muffin recipe tastes like a cross between a chocolate cake and a brownie. You’d never know that there’s pumpkin puree hidden inside! (It’s for texture, not flavor.)

Instead of using dry ingredients, like white whole wheat flour or oat flour, this recipe is flourless, which means it’s also gluten-free. Almond butter and eggs work together to create a fluffy texture you’ll love, with no oil required.

These healthy muffins make a delicious breakfast or snack, when you need something quick to grab. 

Ingredients You’ll Need

healthy chocolate muffin ingredients labeled in glass bowls.

This pumpkin puree in this recipe adds extra nutrients and moisture, without adding a noticeable flavor. If you don’t have canned pumpkin on hand, you could swap it for mashed ripe banana or unsweetened applesauce, but keep in mind that both of those options will change the rich chocolate flavor. 

You could also use Greek yogurt as a substitute if you don’t need a dairy-free recipe. 

chocolate muffins sitting on a white counter.

How to Make Healthy Chocolate Muffins

​1. Mix the wet ingredients. 

In a large mixing bowl, combine the almond butter, pumpkin puree, eggs, coconut sugar, maple syrup, cacao powder, vanilla extract, baking soda, and salt.

Mix well, until the batter looks smooth. Fold in the chocolate chips, if you want a double chocolate muffin.

chocolate muffin batter mixed together in glass bowl.

2. Bake. 

Line a muffin tin with 12 liners, then use a 1/4 cup measure to scoop the batter into each spot. You should get 12 muffins from this recipe.

Sprinkle a few extra chocolate chips on top, if you’d like.

chocolate chips added to the batter and poured into muffin tin.

Bake in the oven at 350ºF for 25 minutes, or until the tops of the muffins rise and look dry on top. If the center of the muffin sinks significantly, that means they probably didn’t cook quite long enough.

You can also test the center of the muffin with a toothpick, if you prefer.

chocolate muffins in the pan before and after baking.

3. Enjoy!

Let the muffins cool in the pan for 20 minutes, then transfer them to a wire rack to finish cooling completely.

Serve the muffins at room temperature, then store any leftovers in an airtight container in the fridge for up to a week. 

chocolate muffin split open on a plate to show the fluffy texture.

Frequently Asked Questions

Do these muffins freeze well?

Yes, you can store the muffins in an airtight container in the freezer for up to 3 months. To thaw, place them in the fridge for up to 48 hours so they can soften again.

Can I use a different sweetener?

You can replace the maple syrup with honey if you prefer, but the honey flavor will be slightly more noticeable. I don’t recommend replacing the granulated sugar with a liquid sweetener, or you might not achieve the same texture, but you can use another granulated sugar if you need to. 

Do I have to use muffin liners? 

If you grease the pan with cooking spray or coconut oil, the muffins will not release quite as nicely. (The muffin liners guarantee they’ll come of out the pan easily.) Without the liners, you’ll probably need to run a knife around the edges to help them release from the pan. 

What if I have different ingredients to use?

You can swap the cacao powder for cocoa powder if that’s what you keep on hand, and you can also use peanut butter instead of almond butter if you prefer. (The peanut butter creates a slightly drier texture.) If you want to try another veggie puree, you can toss raw zucchini in a blender to create a zucchini puree that could be used instead of the pumpkin. 

Want to boost the flavor?

You can add a teaspoon of espresso powder, if you keep it on hand, to emphasize the chocolate taste. For a less-sweet muffin, you can also cut back on the maple syrup, for a darker chocolate flavor.

Looking for more healthy muffin recipes? Try Blender Banana Oatmeal Muffins, Raspberry Chocolate Chip Almond Flour Muffins, or Chocolate Zucchini Muffins, for another variation.

chocolate muffins in pan and on a plate.

Healthy Chocolate Muffins (with Pumpkin!)

4.93 from 81 votes
Healthy Chocolate Muffins have a fluffy texture, without using flour or oil! They taste like a cross between chocolate cake and brownies, with a sneaky veggie hidden inside.
prep5 mins cook25 mins total30 mins
Servings:12

Ingredients
 
 

Instructions

  • Preheat the oven to 350ºF and line a muffin tin with 12 muffin liners. In a large bowl, stir together the almond butter, pumpkin puree, eggs, maple syrup, coconut sugar, cacao powder, vanilla extract, baking soda, and salt. Once the batter looks smooth, fold in the chocolate chips.
  • Use a ¼ cup measure to divide the batter between the 12 prepared muffin cups. Sprinkle a few extra chocolate chips on top, if you like.
  • Bake at 350ºF until the muffins have risen, and the center looks dry, about 25 minutes.
  • Let the muffins to cool in the pan for 20 minutes, then transfer them to a wire rack to cool completely. You can serve them at room temperature, or store them in an airtight container in the fridge for up to a week.

Video

Notes

  • Nutrition information is for 1 of 12 muffins, including the chocolate chips. This information is automatically calculated and is just an estimate, not a guarantee.
  • See the full post above for substitution tips. You can use any other nut butter or fruit/veggie puree in this recipe for a similar texture, but the flavor will change depending on what you use.
  • I haven’t had the chance to test a vegan version of this recipe yet, so I’m not sure if there’s a successful swap for eggs.
Update Note: This recipe used to be called “Paleo Double Chocolate Pumpkin Muffins,” but was updated in January 2023 with a shorter name and updated photos. The recipe has not changed, but you can see the original version here.

Nutrition

Calories: 230kcal | Carbohydrates: 20g | Protein: 6g | Fat: 16g | Saturated Fat: 3g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 8g | Trans Fat: 0.01g | Cholesterol: 27mg | Sodium: 122mg | Potassium: 282mg | Fiber: 4g | Sugar: 11g | Vitamin A: 1631IU | Vitamin C: 0.4mg | Calcium: 94mg | Iron: 2mg
Course: Breakfast
Cuisine: American
Keyword: healthy chocolate muffins

If you try these healthy chocolate muffins, please leave a comment and star rating below letting me know how you like them.

Megan Gilmore leaning on her white countertop.

Megan Gilmore

Hi, I’m Megan. A former fast food junkie trying to make healthy living as easy as possible.

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Comments

  1. Can this be made as a square sheet cake or a loaf? Any idea how that would change the name time or finished product? I made these muffins once with borrowed muffin tins and LOVED them. I don’t have those muffin tins and was hoping to make again for an event tomorrow!

  2. These are delicious! I used 1/2 cocoa and 1/2 cacoa and omitted the sugar. Plenty sweet! The batter tastes just like brownie batter. I licked the entire bowl clean!

  3. I love these muffins and so does the rest of my family. Really delicious! Megan, I used to work with your mother-in law at the library and I miss chatting with her since she moved away. I was already familiar with your website before I met her, but she recommended I check out your book, which is wonderful. Thanks for the great recipes!!!

  4. These muffins are AMAZING! I am 1 month into a dairy-free, grain-free, sugar-free lifestyle, and have been searching for simple, healthy, and yummy treats. The first bite was heavenly. (The rest of the bites were heavenly, too!) Thank you SO MUCH for this recipe!

  5. I made this before they came out perfect. I made them a second time and all the muffins sunk in? I don’t know what i did? Help?

    1. Flourless muffins tend to sink if they don’t cook all the way through. It could just be that the second batch needed a few more minutes in the oven.

      1. They didn’t look sunken in until they started to cool. Any tips to tell if baking is needed a bit longer since they appear puffed on the top? Thank you so much! These are incredible!

  6. I made these with my 3 year old daughter today and they were phenomenal! So rich and moist. Better than traditional cupcakes with flour and white sugar. My daughter loved them and I can feel good about her eating them given the healthy ingredients. They will be our new go to when we are craving chocolate.

  7. These are incredibly delicious! Moist, fudgy consistency. They taste like they should be bad for you! I added peanut butter chips to mine instead of chocolate chips.

  8. Could applesauce be dubbed for the pumpkin? I have a few apples needing to be used up. These are delicious btw

  9. This recipe makes amazing brownies when put in a slice time and slightly u set so stays fudgy
    I use tahini instead of nut butter because our school hasn’t banned tahini

  10. These are delicious- like a mini brownie/cake! My hubby ate 4!! in one go. (Due to food allergies, he has limited “treat” options, so these were a major hit). Thank you!!!!