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Make these Healthy Pumpkin Chocolate Chip Muffins for the perfect fall treat. They are delicious gluten free pumpkin spice muffins that are made extra sweet with a few chocolate chips.

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.

What kitchen tools will I need to make these gluten free pumpkin muffins?
- Muffin tin
- Muffin tin liners or parchment paper
- Mixing bowls
- Measuring spoons
- Measuring cups
- Liquid measuring cup
- Spatula
- 1.5 tbsp measuring scoop

What ingredients will I need to make these pumpkin spice 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

Let’s make a 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.
Step 4: Enjoy!

How should I store these pumpkin chocolate chip muffins?
Store these healthy pumpkin muffins on the countertop for a couple of days or in the fridge for longer. You can freeze these muffins for later, but be sure to cool them completely before freezing.
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!


Healthy Pumpkin Chocolate Chip Muffins
- Prep Time: 10 minutes
- Cook Time: 30 minutes
- Total Time: 40 minutes
- Yield: 10 muffins 1x
- Category: Snack
- Method: Bake
- Cuisine: American
- Diet: Gluten Free
Description
Spiced healthy pumpkin muffins made a little sweeter with chocolate chips.
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
- 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
- Add eggs, pumpkin puree, maple syrup, and melted and cooled coconut oil to a large mixing bowl and mix together thoroughly
- In a separate mixing bowl combine almond flour, coconut flour, baking powder, baking soda, salt, and pumpkin pie spice
- Fold dry ingredients into wet with a spatula
- Then fold in chocolate chips
- Take 3 tbsp of batter and place in each of 10 muffin tin slots
- Place muffin tin in the oven and bake for 30 minutes
- Remove from the oven and allow to cool slightly in the muffin tin before transferring to a cooling rack to cool fully
Keywords: healthy pumpkin muffins, pumpkin chocolate chip muffins, healthy pumpkin chocolate chip muffins
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!
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This is such helpful information!! Thank you for sharing!!
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!!
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!
Did the substitutions and they came out AMAZING. Thank you for some healthy yet tasty recipes during Quarantine 🙂
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Ah yay!! Thank you for following up! So glad you enjoyed!
These muffins are amazing! Perfect for people that are gluten free – they had an amazing texture and tasted amazing!
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Amazing!! Thank you for the review!!
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.
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Oh amazing!!! so glad to know that spelt flour works!
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?
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
Hi! Can I use all-purpose flour instead? Anything I’d need to change? Thanks!
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.
These are delicious! A great way to use up remaining pumpkin purée!
Yay! so glad you enjoyed!!
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?
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
So so easy and tasty. Great flavor and start amazing. Can’t wait to make again.
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yay! I am so glad. Thank you!!
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.
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ah I love that!! makes me so happy