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Healthy Double Chocolate Muffins

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By: MadelinePosted: 09/13/2022Updated: 09/15/2022

This post may contain affiliate links. Please read my disclosure policy.

These Healthy Double Chocolate Muffins are so delicious and fluffy, no one will know they’re gluten free. Serve these healthy chocolate muffins for dessert or a snack!

side view of healthy chocolate muffins stacked on  a cooling rack

These Double chocolate Chip muffins are the perfect balance of fluffy and rich

I don’t have much of a sweet tooth, but when I am craving something sweet, I want it to be extra chocolaty. Therefore, I created this healthy chocolate chip muffin recipe to taste as close as possible to a slice of rich chocolate cake.

It might shock you to see that I use some pumpkin puree to make these muffins extra moist. They don’t taste like the pumpkin at all, but it gives them extra moisture and rise like a true bakery muffin.

There is just something about reaching for a soft and fluffy muffin as a snack that is so satisfying. My favorite time to enjoy these double chocolate muffins is in the mid afternoon as a little pick me up.

They are so rich and delicious that you could even serve them with a bit of chocolate buttercream on top like a cupcake.

three quarter view of healthy double chocolate muffins on a cooling rack

Kitchen tools

  • Muffin pan
  • Cupcake liners – you can use folded parchment paper instead of the liners
  • Mixing bowls
  • Measuring cups and measuring spoons
  • Liquid measuring cup
  • Mixing spoons

serving Suggestions

Like I said, my favorite way to enjoy these gluten free chocolate chip muffins is in the mid afternoon. They are perfect alongside a cup of coffee or tea.

I love making a batch of my homemade cold brew with a splash of cream. Then, I take a nice break from work with my coffee and muffin.

You could also serve them as part of a brunch spread alongside your favorite savory breakfast items.

chocolate muffin with the wrapper pulled down sitting on a cooling rack on a blue towel

Ingredients

Pumpkin puree is the secret ingredient for making light and fluffy healthy chocolate muffins. This keeps the muffins moist without making them dense.

  • Eggs
  • Pumpkin puree – canned pumpkin, but check that the only ingredient is pumpkin
  • Maple syrup
  • Coconut oil
  • Cocoa powder
  • Baking powder
  • Baking soda
  • Salt
  • Chocolate chips

Ingredient substitutions

It can be difficult to mess with gluten free baking recipes SO I recommend baking the recipe just as it is written above. You can attempt to use plain all purpose flour for this recipe, but you will likely need about a full cup of the flour for it to be equivalent to the coconut flour.

If you want to make this recipe dairy free, simply use dairy free chocolate chips. For a fun spin on the recipe you could also use peanut butter chips or butterscotch chips in place of regular semi sweet chocolate chips.

three quarter view of chocolate chip muffins on a cooling rack

How to make some healthy double chocolate muffins

Step 1: Preheat oven and mix batter

To begin, preheat oven to 350F and line 10 cupcake pan slots with cupcake liners. Next, add eggs, pumpkin puree, maple syrup, and melted coconut oil to a large mixing bowl and mix thoroughly.

Then, in a separate mixing bowl, combine coconut flour, cocoa powder, baking soda, baking powder and sea salt. Fold dry ingredients into wet ingredients and then fold in the chocolate chips.

Step 2: Fill muffin tins and bake

Next, use an ice cream scoop and add 1/4 cup of batter to each of the 10 cupcake mold slots. Then, place in the oven and bake for 26-28 minutes.

Step 3: Cool and enjoy!

Remove them from the oven and allow the healthy chocolate muffins to cool fully before enjoying. Finally, store in an airtight container on the counter for up to 5 days.

side view of a healthy double chocolate muffin with a bite out of it

Storage and Freezing

Once cooked and cooled, store these healthy chocolate muffins in an airtight container at room temperature for up to 5 days. You can also store them in the refrigerator for up to 7 days.

If you want to keep them for longer, you can freeze these muffins for up to 4 months. You can remove them and defrost to enjoy one by one.

Check out these other healthy muffin recipes!

  • Healthy Almond Muffins
  • S’mores Muffins
  • Healthy Blueberry Jam Muffins
  • Healthy Pumpkin Chocolate Chip Muffins

You can find the full recipe below. If you make this recipe, please rate and review it in the comments, or share it with me on Instagram!

pinterest image for healthy double chocolate muffins
Recipe

Healthy Double Chocolate Muffins

★★★★★ 5 from 14 reviews

Make these healthy double chocolate chip muffins with just a few simple ingredients!

Recipe By: Madeline
Prep: 10 minutesCook: 26 minutesTotal: 36 minutes
Print Pin it Rate recipe Save recipe
Servings: 10 muffins 1x

Ingredients

  • 3 eggs
  • 1/2 cup pumpkin puree (canned pumpkin, but make sure pumpkin is the only ingredient)
  • 1/2 cup maple syrup
  • 1/4 cup melted coconut oil or any neutral tasting vegetable oil
  • 1/4 cup coconut flour
  • 1/2 cup cocoa powder
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 1/4 tsp salt
  • 1/2 cup chocolate chips

Instructions

  1. Preheat oven to 350F and line 10 cupcake tin slots with cupcake liners
  2. Add eggs, pumpkin puree, maple syrup, and melted coconut oil to a large mixing bowl and mix thoroughly
  3. In a separate mixing bowl combine coconut flour, cocoa powder, baking soda, baking powder and sea salt
  4. Fold dry ingredients into wet ingredients and then fold in the chocolate chips
  5. Add 1/4 cup of batter to each of the 10 cupcake mold slots
  6. Place in the oven and bake for 26-28 minutes
  7. Remove from the oven and allow them to cool fully before enjoying
  8. Store in an airtight container on the counter for up to 5 days
This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition data is gathered primarily from the USDA Food Composition Database, whenever available, or otherwise other online calculators.
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Healthy Double Chocolate Muffins?

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About Madeline

Hi, I'm Madeline! I am so excited to share my healthy and approachable recipes with you. Here you will find simple, comforting recipes that the whole family will enjoy. Turn on your favorite playlist or podcast and let's get cooking!

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Recipe rating ★☆ ★☆ ★☆ ★☆ ★☆

  1. Molly says

    Posted on 6/25 at 12:25 pm

    As someone with an autoimmune disease, I have (temporarily, I hope) eliminated several foods from my diet and have been searching for a healthier sweet treat to satisfy my cravings. These muffins were PERFECT. The pumpkin base makes them moist and fluffy and they certainly satisfy my chocolate and sweet cravings. I didn’t have chocolate chips on hand, so I left those out but these muffins are still delicious. Definitely recommend!

    ★★★★★

    Reply
    • Madeline says

      Posted on 6/26 at 11:20 am

      THank you for sharing! I am in the exact same situation so I FEEL YOU. annoying to have to limit yourself, but SO nice to find alternatives.

      Reply
  2. Leah G says

    Posted on 7/7 at 9:54 pm

    OMG!!!! These are AMAZING! Made them for a trip and they traveled well and really hit the sweet tooth craving. Definitely making these gems again.

    Reply
    • Madeline says

      Posted on 7/8 at 7:28 am

      ah yay! So glad!! They definitely cure my cravings

      Reply
  3. Veronica says

    Posted on 7/9 at 4:43 pm

    I made these this morning, and they were amazing! They tasted just like chocolate cake. I did not detect any extra flavors (although they wouldn’t be necessarily bad, just not flavors that would be in chocolate cake) such as pumpkin or maple syrup. They are moist and chocolaty and just what I have been craving. I have recently dropped refined sugar and gluten from my diet, and I’m happy to have found this recipe to fulfill my chocolate muffin craving! Thank you!

    ★★★★★

    Reply
    • Madeline says

      Posted on 7/11 at 5:00 pm

      Thank you for sharing, Veronica! and I agree, the cocoa really masks the other flavors to make a rich and chocolatey muffin

      Reply
  4. Alexis Mauger says

    Posted on 7/14 at 10:09 am

    These are so delicious! My boyfriend said these were one of the best muffins he’s ever eaten. So easy to make and they taste amazing!

    ★★★★★

    Reply
    • Madeline says

      Posted on 7/14 at 2:45 pm

      Thank you for sharing!! Boyfriend approved is a high honor in the world of healthy baking

      Reply
  5. Mar says

    Posted on 8/2 at 3:39 pm

    Made these last night and they were perfect! Ate one immediately and it was so moist. Today for a snack I had one and topped it with probiotic cocoyo and fresh blueberries – so good. Appreciate that this recipe is dairy free, grain free, and nut free but still has eggs and no fake sugars. Whenever you eliminate everything from a baked good like this I feel that it really never satisfies the craving. Keeping the eggs and maple syrup made these perfect and they satisfy the craving for those chocolate muffins from Costco.

    ★★★★★

    Reply
    • Madeline says

      Posted on 8/3 at 11:13 am

      I am SO glad! Thank you for sharing! I agree that you still want things to taste like a treat 🙂

      Reply
  6. Marygrace says

    Posted on 8/12 at 9:52 pm

    I made these for my family over the weekend and everyone RAVED about them, especially my mom! She and I are both gluten and dairy intolerant so we were thrilled to find a recipe that accommodated our needs AND satisfied our sweet/chocolate cravings. Loved the texture, the taste, and the simplicity of the ingredients!

    ★★★★★

    Reply
    • Madeline says

      Posted on 8/13 at 7:52 am

      This makes me SO happy!! I love that recipes can work for dietary restrictions and still be delicious. Thank you for sharing!!

      Reply
  7. Colleen M says

    Posted on 9/14 at 8:52 pm

    These muffins are so unbelievably delicious. I highly recommend them if you love anything chocolate! I can’t believe they are gluten free. My picky husband and GF nephew devour these when I make them.

    ★★★★★

    Reply
    • Madeline says

      Posted on 9/15 at 12:15 pm

      Yay! Thank you for sharing!! SO happy your family enjoyed them

      Reply
  8. Pegj51 says

    Posted on 10/31 at 1:07 pm

    Delicious! Thank you! For mini muffins, what would be the baking time?

    Reply
    • Madeline says

      Posted on 10/31 at 1:13 pm

      Hi! 17 minutes should be good!

      Reply
  9. Johanna S says

    Posted on 11/7 at 3:06 pm

    Do moist and chocolatey! Someone posted on Instagram that they used 1c almost flour instead of coconut flour and it’s perfect! I usually don’t have coconut flour in my home so it worked out. I only needed to bake mine for 22 minutes instead of 32. I say just keep an eye out on your muffins and when you smell the chocolate, just check on it. Deff making again

    ★★★★★

    Reply
    • Madeline says

      Posted on 11/8 at 9:06 pm

      Amazing!! Thank you!!

      Reply
  10. Julie says

    Posted on 12/28 at 6:07 pm

    Love these muffins!! Great flavor and texture. I followed the recipe exactly and I wouldn’t change a thing! Just trust the recipe, folks 🙂

    ★★★★★

    Reply
    • Madeline says

      Posted on 12/28 at 9:19 pm

      wonderful!! I agree 🙂 trust the recipe!!

      Reply
  11. Lindsey Wherley says

    Posted on 1/17 at 12:02 pm

    If you want a healthy muffin that is super deceiving- THIS IS IT! So yummy, moist, and delicious. Tastes just like homemade chocolate cake that I grew up with – only much healthier!
    Would 100% recommend, surely a crowd pleaser!

    ★★★★★

    Reply
    • Madeline says

      Posted on 1/18 at 12:46 pm

      love that!! Thank you!

      Reply
  12. Virginia says

    Posted on 1/18 at 8:37 pm

    Hi! I want to make these but I do not have coconut (or almond) flour. What do you recommend as a replacement?

    Reply
    • Madeline says

      Posted on 1/18 at 9:06 pm

      Hi! I’ve never personally tried anything else, but perhaps you could try 1/2 cup of AP flour.

      Reply
  13. Ellen Willing says

    Posted on 5/3 at 1:14 pm

    Oh my goodness these are DELICIOUS! I used rice flour instead of coconut flour and they still turned out great. Such a nice little treat for after dinner dessert or before bed cravings!

    Reply
    • Madeline says

      Posted on 5/4 at 8:38 pm

      wonderful!! thank you so much!!

      Reply
  14. MM Gayhardt says

    Posted on 6/9 at 10:33 am

    Made these to satisfy my sweet tooth after dinner and they did not disappoint (even had one for breakfast)! I subbed almond flour for the suggested amount of coconut flour and it worked perfectly! Will def be making again!

    ★★★★★

    Reply
    • Madeline says

      Posted on 6/17 at 9:48 pm

      yay!! thank you so much!

      Reply
  15. Julie says

    Posted on 6/9 at 11:21 am

    These muffins are SO GOOD! I didn’t have coconut flour on hand, but I was craving these muffins so I substituted regular flour. If one ingredient is holding you back from trying these, get creative!

    ★★★★★

    Reply
    • Madeline says

      Posted on 6/17 at 9:47 pm

      aww I love that! thank you!

      Reply
  16. Amanda A. says

    Posted on 6/9 at 4:12 pm

    ANOTHER GREAT RECIPE!!! I just baked a batch and I’ve already eaten 3!!! So good!!

    ★★★★★

    Reply
    • Madeline says

      Posted on 6/17 at 9:16 pm

      wonderfuL!! thank you so much!

      Reply
  17. Mary Margaret Gayhardt says

    Posted on 2/2 at 7:24 pm

    I think I have made these about a dozen times now! Perfect recipe for a Sunday bake sesh if you want something sweet for the days ahead and love them any time of day 🙂

    ★★★★★

    Reply
    • Madeline says

      Posted on 2/3 at 5:28 pm

      thanks so much!

      Reply
  18. Trina says

    Posted on 9/11 at 1:26 pm

    Can you replace the eggs? My friend is Vegan.

    Reply
    • Madeline says

      Posted on 9/15 at 1:08 pm

      I haven’t personally tried, but if you do I would try flax eggs

      Reply
  19. Madeline Burns says

    Posted on 9/15 at 2:25 am

    These muffins were EXACTLY the moist, decadent feeling treat I was looking for! Lovely texture, and great light sweetness with the right amount of chocolatey-ness. Approved by my 12 year old with a “so yum mum!”.

    ★★★★★

    Reply
    • Madeline says

      Posted on 9/15 at 1:06 pm

      yay!! so glad you both enjoyeed!!

      Reply
  20. Franceaz says

    Posted on 9/21 at 12:17 pm

    These look so delicious! Could I use bananas in place of the pumpkin, and would 2 bananas be about the same amount? Thank you for the recipe!

    Reply
    • Madeline says

      Posted on 9/25 at 1:20 pm

      Depends on size of banana! but yes id just mash and measure to make sure you have enough!!

      Reply

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