Healthy Chocolate Muffins

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These healthy chocolate muffins are dairy-free and made with whole wheat flour, applesauce and naturally sweetened with maple syrup. They’re fudgy, rich, perfectly moist and absolutely delicious.

Sweet treats can be healthy! I love taking my favorite sweets and putting my spin on them so I’m not left with a blood sugar spike and an upset stomach. I made a few simple swaps for an EBF-approved version of a chocolate muffin!

A birds eye view of 4 chocolate chip muffins on a wire rack.

Why You Need to Make These Healthy Chocolate Muffins

  • Healthy + chocolate in one recipe? What more could you ask for! These delicious muffins are made with upgraded ingredients so you don’t leave with a sugar high after indulging.
  • They’re perfectly moist and fudgy… the best kind of chocolate muffins.
  • I like eating them for breakfast, snack or dessert! Yes, chocolate for breakfast is fair game in this case!
  • This is a great recipe to make with kids! They’ll love helping you pour ingredients into the bowl and mix and will obviously love the end result.
Ingredients measured out to make chocolate muffins: applesauce, salt, baking soda, baking powder, vanilla, cocoa powder, coconut oil, eggs, whole wheat pastry flour, maple syrup, chocolate chips and non-dairy milk.

Ingredients Needed

  • whole wheat pastry flour – whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy texture that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour. If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • cocoa powder – cocoa powder makes these muffins chocolate flavored! Make sure you use unsweetened cocoa powder.
  • baking soda and baking powder – helps the muffins rise.
  • salt – brings all of the flavors together.
  • eggs – helps bind the liquid and oil together. Make sure your eggs are at room temperature or they can make the coconut oil solidify while mixing.
  • maple syrup – the natural sweetener of choice for these muffins. I haven’t tried making these with honey but that should work as well.
  • unsweetened applesauce – helps reduce the amount of oil you need while still keeping the muffins super moist. Make homemade applesauce or use store-bought unsweetened applesauce.
  • non-dairy milk – any dairy-free milk works for these muffins! I typically use unsweetened almond milk.
  • coconut oil – helps make the muffins moist and fluffy! The oil also helps prevent the muffins from sticking to the liners.
  • vanilla extract – a flavor enhancer.
  • chocolate chips – add a little more chocolate to these muffins with chocolate chips! I like using Lily’s dark chocolate chips because they are low in calories and sugar.
Collage of four photos showing the steps to make healthy chocolate muffins: mixing the dry ingredients, mixing the wet ingredients, mixing the two together and then adding batter to a muffin tin.

How to Make Healthy Chocolate Muffins

Start by mixing the flour, cocoa powder, baking soda, baking powder and salt in a medium bowl. In a separate bowl, crack the eggs and whisk a little before adding the other wet ingredients. Then add the maple syrup, applesauce, milk, oil and vanilla and whisk again until combined. Add the wet ingredients to the dry ingredients and stir until just combined. Don’t overmix or your muffins will end up really dense… we don’t want that! Gently fold in the chocolate chips. Pour the batter evenly between 12 muffin tins that are lined with paper or silicone liners. Bake in an oven preheated to 350ºF for 20-22 minutes or until a toothpick inserted into the center of the muffin comes out clean. Let the muffins cool in the tin for 5 minutes before removing to cool completely on a wire rack.

Close up of a chocolate chip muffin on a wire rack.

Tips For Success

  • It’s super important to make sure you’re using room temperature milk, eggs, maple syrup and applesauce! If any of these ingredients are cool or cold, the coconut oil will solidify and create clumps. If you notice this happening, you can set the mixing bowl on the warm part of your stovetop as the oven preheats or set the mixing bowl in a larger bowl of hot water until the coconut oil melts again. You just want to make sure you don’t get the batter too hot or the eggs will start cooking. Here’s a guide for how to bring things like butter, eggs and yogurt to room temp.
  • When combining your dry and wet ingredients make sure you mix until just combined and don’t over-mix, otherwise your muffins could turn out too dense or rubbery. It’s even okay if there are a few streaks of flour remaining as they’ll get mixed in when you stir in the chocolate chips.
  • I highly recommend using silicone muffin liners or parchment baking cups for the best results and to prevent the muffins from sticking.
  • Let the muffins cool for a few minutes in the muffin tin and then remove to let cool completely on a wire rack. Don’t leave the muffins in the muffin tin for too long because they’ll continue to bake and could dry out!
  • If using paper liners, make sure to let the muffins cool completely before trying to remove the liners otherwise your muffins will likely stick. If you’re trying to speed up the process, place your muffins in the fridge to cool down quicker.

Frequently Asked Questions

Can I use all-purpose flour?

Yes! All-purpose flour will work just fine in place of whole wheat pastry flour.

Can I make these muffins gluten-free?

I haven’t tested a gluten-free version of these muffins, but I would imagine using a 1:1 gluten-free all-purpose flour would work just fine in place of the whole wheat pastry flour. My favorite brand is Bob’s Red Mill gluten-free 1:1 all-purpose flour.

What can I use instead of applesauce?

Bananas would be the best substitute for the applesauce. 2 small bananas should equal 1/2 cup mashed. Pumpkin puree or sweet potato puree would also work in place of the applesauce.

Is there an egg substitute?

I haven’t tested an egg-free version of these muffins, but let me know if you decide to experiment in the comments below! I would imagine using two flax eggs or chia eggs in place of the regular eggs would work just fine. 

How do I prevent my muffins from sticking to the liners?

I highly recommend using silicone muffin liners or parchment baking cups for the best results and to avoid the muffins from sticking too much. I also recommend spraying your liners with a little cooking spray. Also, make sure to let your muffins cool completely before trying to remove the liners otherwise they could stick. If you want, you can pop the muffins in the fridge to cool for an hour or so before removing the liners.

A healthy chocolate chip muffin cut in half. A hand is holding up the half so you can see the gooey chocolate chips inside.

How to Store Healthy Chocolate Muffins

After allowing the muffins to cool completely, store them in an airtight container for 3-4 days at room temperature or for up to 1 week in the refrigerator. For longer storage, you can freeze these muffins for up to 3 months in a freezer-safe container or bag. I like to use my Stasher bags for easy storage. To defrost, place muffins in the fridge overnight, at room temperature or defrost in the microwave.

More Muffin Recipes to Try

Be sure to check out all of my muffin recipes and the full collection of breakfast recipes here on EBF!

Healthy Chocolate Muffins

5 from 26 votes
These healthy chocolate muffins are dairy-free and made with whole wheat flour, applesauce and naturally sweetened with maple syrup. They're fudgy, rich, perfectly moist and absolutely delicious.
A birds eye view of 4 chocolate chip muffins on a wire rack.
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Servings 12 muffins

Ingredients

Instructions
 

  • Preheat the oven to 350°F. Place 12 paper or silicone liners in your muffin tin.
  • In a medium mixing bowl combine the flour, cocoa powder, baking soda, baking powder and salt.
    A wooden spoon is mixing together flour, cocoa powder, baking soda, baking powder and salt in a bowl.
  • In a separate bowl, crack the eggs and whisk. Add maple syrup, applesauce, milk, oil and vanilla and whisk until combined.
    Eggs being whisked together with maple syrup, apple sauce, milk, oil, and vanilla.
  • Add the wet ingredients to the dry and whisk together until just combined. Don’t overmix! Fold in the chocolate chips.
    The wet and dry ingredients have been mixed together and chocolate chips have been added to the batter.
  • Pour batter evenly between 12 muffin tins. I used ¼ cup to measure the batter.
    The batter has been poured into the lined muffin tin.
  • Bake for 20-22 minutes or until a toothpick inserted in the center of the muffin comes out clean.
  • Let muffins cool in the tin for about 5 minutes or so, then remove and let cool completely on a wire rack.

Equipment

Nutrition

Serving: 1muffin Calories: 187kcal Carbohydrates: 29g Protein: 4g Fat: 8g Saturated Fat: 5g Monounsaturated Fat: 1g Cholesterol: 33mg Sodium: 157mg Potassium: 88mg Fiber: 4g Sugar: 10g
Course: Breakast
Cuisine: American
Keyword: healthy chocolate muffins

DID YOU MAKE THIS RECIPE?

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Recipe Rating




    24 comments
    1. Ashley
      January 24, 2023 AT 8:14 am

      5 stars
      Sooooooo good!!!! Perfect balance of sweet and I absolutely LOVE how they aren’t too sweet.Jsut the right touch! I used honey since that’s what I had on hand and no oil. These will be my new go to healthy chocolate muffins 😋 These came out soft and moist. My oven took 10-15 minutes to bake though. Ovens do vary! Make this recipe y’all!!!!!

      1. Brittany Mullins
        January 24, 2023 AT 3:35 pm

        AHH this is great, Ashley. I am so excited to hear that you are loving this recipe and that it is a hit. Thank you so much for coming back and sharing your review + star rating, it means so much to me!

    2. Emma Ringer
      November 3, 2022 AT 12:34 pm

      5 stars
      I absolutely LOVE these and so does my whole family! They taste like such a treat. I’m gluten free so I replaced the whole wheat flour with 2 cups of oat flour and they still turned out perfectly!

      1. Brittany Mullins
        November 3, 2022 AT 5:25 pm

        YUM! I am so excited to hear that this recipe worked out and are a hit, Emma. It’s great to know they also work well with the oat flour. Thank you for sharing your review + star rating, I so appreciate it!

    3. Cloey
      October 30, 2022 AT 5:04 pm

      5 stars
      These are delicious!! Not too sweet, which is perfect. I used 1 cup of whole wheat flour and 1/2 cup of all purpose flour with amazing results. These muffins are soft, moist, and fluffy inside. I also used honey instead of maple syrup since we were running low on the syrup. Thanks for another amazing recipe! All of your muffin recipes that I’ve tried have turned out great 🙂

      1. Brittany Mullins
        October 31, 2022 AT 10:03 am

        Ah YAY! I am so excited that you are loving this recipe, Cloey. Thank you so much for coming back and sharing your review + star rating, I so appreciate it.

    4. Jennifer
      March 7, 2022 AT 4:45 pm

      5 stars
      I made these using Pamela’s gluten free baking mix and they are to die for!!! Wow, rich chocolate but not the rich calories! Having two myself before the kids get home! Ha! Thank you EBF!

      1. Brittany Mullins
        March 8, 2022 AT 8:34 am

        Woo! Love to hear that, Jennifer! Thanks for sharing and leaving a review, it means the world to me.

    5. helene
      February 20, 2022 AT 4:51 am

      5 stars
      excellent post thank you for sharing

Parchment paper lined with protein balls.

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