Healthy Pumpkin Chocolate Chip Muffins

Nothing beats a delicious muffin! Light, fluffy, and moist, this Healthy Pumpkin Chocolate Chip Muffins checks all the boxes. Made with 10 ingredients, these muffins are dairy-free, paleo friendly, and gluten-free as well as freezer friendly.

Pumpkin season is in fully swing! Did you see my recent Healthy Pumpkin Chocolate Chip Bread recipe? Well, today I’m back with another pumpkin flavoured recipe, this time — muffins! These are such a great grab and go snack or breakfast, when in a rush, we just grab one to enjoy on our walk to school.

Even better is that these healthy pumpkin chocolate chip muffins are freezer friendly so you can make a large batch and enjoy whenever you chose to in the upcoming months. It makes the holiday season so easy as sometimes it’s so busy, we don’t get a chance to prep some healthy treats for ourselves.

A Pumpkin Muffin Recipe for Everyone

While this muffin recipe is dairy-free, paleo friendly, and gluten-free, it can easily be modified to be Keto friendly and low-carb as well. All you have to do is swap out the coconut sugar. Information for that will be down below in the recipe variation section. It’s a recipe that everyone can enjoy!

These pumpkin chocolate chip muffins are also great for bake sales and school parties as not only are they healthy, it is a nut-free recipe as well. They can be made ahead of time so you don’t have to frantically bake these the night before. However, if your kiddo informs you of a bake sale the night before, not to worry, these healthy pumpkin chocolate chip muffins only take 40 minutes from start to finish so you can whip up a batch in a jiffy.

If you’re looking for more muffin recipes to enjoy, try my Low-Carb Chocolate Muffins Recipe, Low-Carb Lemon Blueberry Blender Muffins, Almond Flour Cranberry Muffins, and Gluten-free Carrot Muffins.

two healthy pumpkin chocolate chip muffins stacked on top of each other.

How to Make this Healthy Pumpkin Chocolate Muffin Recipe

Ingredients

close up of healthy pumpkin chocolate chip muffin

Instructions

Prep the Oven and Pan

  1. Preheat oven to 350ºF and line a muffin tin with paper liners or use silicone muffin tin. Set aside.

Mix the Wet Ingredients and Dry Ingredients Separately

  1. In a large bowl, mix together eggs, coconut sugar, pumpkin puree and eggs.
  2. In a medium bowl add almond flour, coconut flour, baking soda, baking powder, pumpkin pie spice and salt.
  3. Mix everything together until all is combined then gently fold in the chocolate chips.

Fill the Muffin Tin and Bake

  1. Divide the batter among the prepared muffin cups.
  2. Sprinkle with additional chocolate chips as desired. This gives it more of a “cafe-style” look with the chocolate chips on top!
  3. Bake for 20-25 minutes, until the tops of the muffins are set.
  4. Let cool before enjoying

6 healthy pumpkin chocolate chip muffins on a serving board

Tips and Notes On Making the Perfect Healthy Pumpkin Chocolate Chip Muffins

  • Baking times may vary because ovens vary in power and efficiency. To check if your healthy pumpkin chocolate chip muffins has baked through, poke a toothpick into them. When removed, if the toothpick comes out clean, it’s done baking. If there is batter on it, continue to bake.
  • Only fill each muffin cups three-quarters of the way of the muffin liners. It’s about two and a half tablespoon per muffin cups.
  • If you’d like to make this healthy pumpkin chocolate muffin ahead of time, you can make the batter in advance and place in the fridge for up to one day beforehand.
  • Be careful not to over mix the batter. Too much mixing will cause the pumpkin muffins to come out dense instead of light and fluffy.

How to Store and Freeze Leftover Healthy Pumpkin Chocolate Chip Muffins

  • Store leftover pumpkin chocolate chip muffin in the fridge in an airtight container for up to a week. If you are storing it on the counter, it’ll last 3 days.
  • Freeze leftovers in a freezer safe bag (be sure to squeeze all the air out) after being wrapped in plastic-wrap for up to 3 months. Thaw in the fridge and bring to room temperature before enjoying or microwave thawed muffins to warm up!

Recipe Variations For These Pumpkin Muffins

  • To Make This Keto & Low-carb: swap coconut sugar for xylitol sweetener. There shouldn’t be conversion needed and can be substituted 1:1.
  • Chocolate chips can be swapped with any types of “chips” such as white chocolate chips, butterscotch chips, caramel chips, etc in this healthy pumpkin chocolate chip muffin. You can even do half-half mix of two flavours!
  • Muffins can also be topped with other items such as coconut flakes, chopped nuts, seeds, dried fruit, etc.

More Pumpkin Baked Goods You May Enjoy

Healthy Pumpkin Chocolate Chip Muffins

Yield: 12 muffins
Prep Time:
10 mins
Cook Time:
20 mins
Resting Time:
40 mins
Nothing beats a delicious muffin! Light, fluffy, and moist, this Healthy Pumpkin Chocolate Chip Muffins checks all the boxes. Made with 10 ingredients, these muffins are dairy-free, paleo friendly, and gluten-free. 
Print Recipe
5 from 3 votes

Ingredients

Instructions

  1. Preheat oven to 350ºF. Line a muffin tin with paper liners or use silicone muffin tin. Set aside.

  2. In a large bowl, mix together eggs, coconut sugar, pumpkin puree and eggs.
  3. In a medium bowl add almond flour, coconut flour, baking soda, baking powder, pumpkin pie spice and salt. Mix everything together until all is combined.
  4. Fold in chocolate chips. Divide the batter among the prepared muffin cups. This is very important: fill each muffin cups three-quarters of the way. It’s about two and a half tablespoon per muffin cups. The dough will be a bit thick, but it will work perfectly. Sprinkle with additional chocolate chips as desired.
  5. Bake for 20-25 minutes, until the tops of the muffins are set and a toothpick inserted in the center comes out clean.
  6. Place the pan on a wire rack and let the muffins cool completely. It’s about 30 minutes. Enjoy!

Recipe Notes

*you can use xylitol for Keto and low-carb diets.
Course: Breakfast
Cuisine: American
Keyword: Almond Flour Muffins, healthy pumpkin muffins, Pumpkin Muffins

Nutrition Information

Amount per serving (1/12) — Calories: 268, Fat: 15g, Saturated Fat: 1g, Cholesterol: 48mg, Sodium: 191mg, Potassium: 399mg, Carbohydrates: 26g, Fiber: 3g, Sugar: 21g, Protein: 8g

If you make this recipe, follow @primaverakitchen on Instagram, snap a photo and hashtag it #primaverakitchen. I'd love to see what you're making!

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Healthy Pumpkin Chocolate Chip Muffins