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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 turned best-selling cookbook author. I create healthy recipes made with simple ingredients to make your life easier.

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Comments

  1. These muffins are amazing. I love them. It’s like eating chocolate. Back when I used to eat box.cake there is that amazing texture well these muffins are even better.

  2. Megan, these are amazing! I used cacao powder instead of cocoa. I made them as a desert for Thanksgiving and they were devoured by everyone. It was great to have a healthier alternative. Thanks so much for sharing!

  3. I made these muffins this morning in a mini muffin pan and they turned out great. I sprayed paper liners with coconut oil and baked for 15 min @ 350. Didn’t stick to the papers at all. They are delicious and so much like a traditional muffin. Kid and husband approved. Thank you for another great
    recipe 🙂

  4. I am sadly off nuts for the foreseeable future, but these looked so amazing that I decided to swap out the almond butter for sunflower seed butter. I used the Trader Joe’s brand, which although delicious, has a sweetener, and it made the muffins a little too sweet for my taste. They were nonetheless delicious — perfect texture and flavor — and I will definitely make them again. Next time I will plan to make my own seed butter, however, to control the sweet factor. A definite winner!

  5. What is the nutritional value /information of this recipe? Trying to watch sugar intake along with glutton free. Would be nice if had that on your recipes.

  6. Recently stumbled upon the chocolate & pumpkin combo and by was I pleasantly surprised!!!!! Struggling through the worst first trimester sickness (all day sickness) and trying to find foods that um, stay down? It’s odd because these would work. Perfect foods like veggies and chicken make me gag now!

    1. Oh, congratulations on your pregnancy!!! I didn’t want any veggies during my first trimester, either. I think I lived off of bagels and pizza!! Both of which are totally unappealing to me now– anything I ate during my first trimester I hated by the time I reached my third trimester. Ha! Hope you feel better soon. 🙂

  7. Sounds yummy! Could you substitute honey for maple syrup. And, have you tried making in a bread pan instead of muffin cups?

    1. I bet using honey in place of maple syrup would work fine. I’m not sure how this would work baked in a pan, though. The edges may get dry by the time the middle set, but that’s just a guess.

    2. I bake it in a pan all the time it makes a great bread!!! it needs to bake longer though. 45 minutes did it in my oven. I’d recommend checking it every few minutes after 45 if it’s not done!

      1. I do this as well and make a snack cake. I add pecans or walnuts and white chocolate chips. It is delicious as this is one of my favorite recipes. You are right it takes a bit longer to cook, about 30ish minutes. I just checking after that at intervals of time to determine when it is done.