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Healthy Pumpkin Chocolate Chip Muffins

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By: MadelinePosted: 10/15/2020Updated: 09/23/2021

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

Make these Healthy Pumpkin Chocolate Chip Muffins for the perfect fall treat. These healthy pumpkin muffins are made extra sweet with a few chocolate chips.

Pumpkin chocolate chip muffins on a serving plate

Healthy pumpkin muffins are even better when you add chocolate chips

When I was a freshman in college I had a super long walk from one part of the campus to another. On Fridays I would treat myself to a massive pumpkin chocolate chip muffin and savor it as I walked.

Now whenever I have a pumpkin spice muffin I remember that time in my life. I found a can of pumpkin in my pantry last week and even though its not the fall, I went to town making a bunch of pumpkin recipes.

These healthy pumpkin chocolate chip muffins are the only sweet recipe that I came up with. These muffins are a slightly sweet and spiced snack or breakfast that are perfect with a cup of coffee.

How to serve

I like to serve these healthy pumpkin muffins as a quick and easy breakfast. Slather them with some creamy peanut butter or almond butter for an extra boost of protein.

They are also perfect as an afternoon pick me up with a cup of coffee. I like to make a pumpkin cream cold brew with this homemade pumpkin spice syrup.

Serve these chocolate chip pumpkin muffins alongside the cookies and pies at thanksgiving dinner. They are perfect for little kids to grab and go.

Side view of  a pumpkin chocolate chip muffin on a cooling rack

What kitchen tools will I need to make these almond flour pumpkin muffins?

  • Muffin tin
  • Muffin tin liners, parchment paper or cooking spray
  • Mixing bowls
  • Measuring spoons
  • Measuring cups
  • Liquid measuring cup
  • Spatula
  • 1.5 tbsp measuring scoop

If you run out of paper muffin tin liners, you can easily make your own with parchment paper. Cut parchment into 5″x5″ squares.

Then, press them down into muffin tins and crease the edges. The healthy pumpkin muffin batter will weigh down the paper and create a little cup.

tip for perfect healthy pumpkin muffins

If you want perfectly formed muffins, spray the inside of the muffin cups or muffin liners with cooking spray before you pour the batter into them. Then, when they are finished, the muffin comes out clean.

Above view of healthy pumpkin muffins on a cooling rack

What ingredients will I need to make these pumpkin chocolate chip muffins?

You will be amazed how easy it is to make these gluten free pumpkin spice muffins with just a few basic ingredients. I recommend using the mixture of almond flour and coconut flour for the best grain free muffin texture.

  • Eggs
  • Pumpkin puree
  • Maple syrup
  • Coconut oil
  • Almond flour
  • Coconut flour
  • Baking soda
  • Baking powder
  • Salt
  • Pumpkin pie spice
  • Chocolate chips

Is canned pumpkin and pumpkin puree the same thing?

Yes! Canned pumpkin and pumpkin puree are usually the same thing. Check the can and make sure that the only ingredient is pumpkin.

You do not want to use canned pumpkin pie filling for this recipe because it is canned pumpkin mixed with other ingredients.

Make them dairy free

It is super easy to make these healthy pumpkin muffins dairy free. Just replace the semi sweet chocolate chips with dairy free chocolate chips.

You can also leave the chocolate chips out completely and replace them with raisins or dried cranberries. If you like a crunch in your muffins, mix some walnut pieces into the batter.

Three quarter close up view of healthy pumpkin muffins

Let’s make Healthy Pumpkin Chocolate Chip Muffins!

Step 1: Mix wet ingredients

First, preheat oven to 350F and line muffin tin with liners. Then, add eggs, maple syrup, coconut oil, and pumpkin puree to a large mixing bowl. Mix thoroughly.

Step 2: Fold in dry ingredients and chocolate chips

Next, add almond flour, coconut flour, baking powder, baking soda, pumpkin pie spice, and salt to a separate mixing bowl and mix thoroughly. Fold fry ingredients into wet and mix with a spatula. Then, fold the chocolate chips into the batter.

Step 3: Bake and cool muffins

Next, scoop 3 tbsp of batter into each of 10 muffin tins. Place in the oven and bake at 350F for 30 minutes. Finally, remove from the oven and cool on baking rack.

Side view of almond flour pumpkin muffins on a cooling rack

How should I store these pumpkin chocolate chip muffins?

Allow these healthy pumpkin muffins to cool completely. Then, store on the countertop for a couple of days in an airtight container.

Store them in the fridge for up to one week. Reheat them in the toaster oven or on the stove top sliced in half.

You can freeze these muffins for up to three months. Defrost them individually in the fridge before reheating them.

Check out these other healthy muffin recipes!

  • Healthy Double Chocolate Muffins
  • Mini Chocolate Chip Banana Muffins
  • Healthy Carrot Cake Muffins
  • S’mores 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!

Image for pinning healthy pumpkin muffins recipe on Pinterest
Recipe

Healthy Pumpkin Chocolate Chip Muffins

★★★★★ 5 from 9 reviews

Spiced healthy pumpkin muffins made a little sweeter with chocolate chips.

Recipe By: Madeline
Prep: 10 minutesCook: 30 minutesTotal: 40 minutes
Print Pin it Rate recipe Save recipe
Servings: 10 muffins 1x

Ingredients

  • 3 eggs
  • 1/2 cup pumpkin puree
  • 1/2 cup maple syrup
  • 1/4 cup melted coconut
  • 1 1/2 cups almond flour
  • 2 tbsp coconut flour
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 2 tsp pumpkin pie spice
  • 1/2 cup chocolate chips

Instructions

  1. Preheat oven to 350F and line 10 muffin cups in a muffin tin with liners – if you don’t have liners you can use squares of parchment paper
  2. Add eggs, pumpkin puree, maple syrup, and melted and cooled coconut oil to a large mixing bowl and mix together thoroughly
  3. In a separate mixing bowl combine almond flour, coconut flour, baking powder, baking soda, salt, and pumpkin pie spice
  4. Fold dry ingredients into wet with a spatula
  5. Then fold in chocolate chips
  6. Take 3 tbsp of batter and place in each of 10 muffin tin slots 
  7. Place muffin tin in the oven and bake for 30 minutes
  8. Remove from the oven and allow to cool slightly in the muffin tin before transferring to a cooling rack to cool fully
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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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. Sarah S says

    Posted on 4/9 at 3:39 pm

    Just made this recipe during “quarantine kitchen” (Passover edition) with mashed sweet potato in place of pumpkin because I didn’t have any pureed pumpkin. The muffins are delicious. Very moist and the pumpkin pie spice is just right! Because I knew the mashed sweet potato would add a bit more sweetness, I used 1/4 C apple sauce + 1/4 C maple syrup instead of 1/2 C maple syrup.

    Definitely will be making these again. A perfect muffin base! Thanks!

    ★★★★★

    Reply
    • Madeline says

      Posted on 4/9 at 4:43 pm

      This is such helpful information!! Thank you for sharing!!

      Reply
  2. Aarti Bains says

    Posted on 4/9 at 6:13 pm

    Hi! I don’t have coconut flour, can I use all almond flour instead? I also was going to sub honey for maple syrup if that is okay. Thanks!!

    Reply
    • Madeline says

      Posted on 4/9 at 7:00 pm

      Hi you can use all almond but you might have to use a bit extra to make sure they aren’t too wet! And honey will work fine!

      Reply
      • Aarti says

        Posted on 4/10 at 3:07 pm

        Did the substitutions and they came out AMAZING. Thank you for some healthy yet tasty recipes during Quarantine 🙂

        ★★★★★

        Reply
        • Madeline says

          Posted on 4/10 at 5:16 pm

          Ah yay!! Thank you for following up! So glad you enjoyed!

          Reply
  3. Ariana Abdulmassih says

    Posted on 4/11 at 10:31 am

    These muffins are amazing! Perfect for people that are gluten free – they had an amazing texture and tasted amazing!

    ★★★★★

    Reply
    • Madeline says

      Posted on 4/13 at 11:34 am

      Amazing!! Thank you for the review!!

      Reply
  4. Gabby says

    Posted on 4/19 at 4:25 pm

    I tweaked the recipe slightly by using spelt flour in place of almond (just a tiny bit less) and a flax egg. Worked perfectly!! So yummy.

    ★★★★★

    Reply
    • Madeline says

      Posted on 4/20 at 7:03 am

      Oh amazing!!! so glad to know that spelt flour works!

      Reply
  5. Zoe Parsigian says

    Posted on 8/24 at 8:45 pm

    Hi! I love this recipe, do you think there would be any way to sub shredded zucchini instead of the pumpkin? Or suggestions of what to add/subtract to make that potentially work?

    Reply
    • Madeline says

      Posted on 8/25 at 10:02 am

      Hi! It’s really hard to say. Could try just adding in the zucchini instead of the pumpkin OR add the zucchini and the pumpkin + a little more flour

      Reply
  6. Liz says

    Posted on 10/2 at 10:22 am

    Hi! Can I use all-purpose flour instead? Anything I’d need to change? Thanks!

    Reply
    • Madeline says

      Posted on 10/2 at 12:09 pm

      Hi I think it would work. Start with 1.5 cups of AP flour. If it seems too liquid still then add a little more.

      Reply
  7. Sarah says

    Posted on 10/8 at 5:25 pm

    These are delicious! A great way to use up remaining pumpkin purée!

    Reply
    • Madeline says

      Posted on 10/8 at 8:51 pm

      Yay! so glad you enjoyed!!

      Reply
  8. Shannon OBrien says

    Posted on 12/6 at 9:49 am

    I have made these multiple times and love them. This morning I was going to double the recipe and realized too late I don’t have enough almond flour. I have coconut flour and was wondering how much I would need to substitute the 1-1/2 cups almond flour? And I also have regular flour, what would be that amount?

    Reply
    • Madeline says

      Posted on 12/6 at 11:22 am

      I worry that too much coconut flour would make these unpleasant! For standard flour you could try between 1 and 1.5 cups total with no coconut flour, but truly not sure how they will turn out because I haven’t personally tried it! Sorry

      Reply
  9. Jess says

    Posted on 12/28 at 7:07 pm

    So so easy and tasty. Great flavor and start amazing. Can’t wait to make again.

    ★★★★★

    Reply
    • Madeline says

      Posted on 12/28 at 9:12 pm

      yay! I am so glad. Thank you!!

      Reply
  10. Katie says

    Posted on 12/29 at 12:05 am

    Made these so many times in quarantine this fall and winter that I know the recipe by heart. So simple, so delicious! Thanks for introducing me to the combo of pumpkin & chocolate, so perfect.

    ★★★★★

    Reply
    • Madeline says

      Posted on 12/30 at 10:50 pm

      ah I love that!! makes me so happy

      Reply
  11. Julie says

    Posted on 9/19 at 9:49 pm

    These are simple and delicious! A great fall snack. I’m not GF so I used 1.5 cups of all purpose flour and they came out great.

    ★★★★★

    Reply
  12. Shannon says

    Posted on 9/24 at 7:18 pm

    These were great! Perfectly delicious. I didn’t change a thing and I will definitely make them again.

    ★★★★★

    Reply
    • Madeline says

      Posted on 9/27 at 5:49 pm

      Thanks Shannon!

      Reply
  13. Erica says

    Posted on 9/26 at 7:38 pm

    These taste amazing, and all my colleagues at work agree! I filled them a little less so that I could get 12 (I have a toddler and wanted some smaller). Definitely adding this to my rotation of muffins!

    ★★★★★

    Reply

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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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