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5 from 10 votes
Home By Course Breakfast Muffins & Breads

Healthy Chocolate Chip Pumpkin Muffins

These Healthy Chocolate Chip Pumpkin Muffins have the best tender, fluffy muffins pumpkin base with gooey chocolate all throughout! They're nutritious and seriously great for breakfast, snack or dessert. Even better, they couldn't be easier to make and are ready in just 30 minutes!

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By: Lauren published: Oct. 05, 2023 updated: Aug. 15, 2024 11 Comments

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

Healthy chocolate chip pumpkin muffins on a cooling rack.
Contents hide
About This Recipe
Why You’ll Love These Healthy Chocolate Chip Pumpkin Muffins
Ingredients and Substitutions
How To Make
How To Store
Baking Tips!
FAQ: Healthy Chocolate Chip Pumpkin Muffins
More Pumpkin Recipes You’ll Love For Pumpkin Season
Healthy Chocolate Chip Pumpkin Muffins
MyFitnessPal Entry
Did You Make This?

About This Recipe

These healthy chocolate chip pumpkin muffins make for one of the best fall recipes! They’re easy to make and versatile, great for breakfast on-the-go, an afternoon snack or even dessert.

This is also a great recipe to freeze so feel free to make a double batch and save some for later. Kids and husbands-alike will have no idea these tasty muffins are lightened up and actually good for you! 

Not sure what to do with leftover pumpkin? Explore these 15+ healthy pumpkin recipes. Or for more muffins, try my peanut butter banana muffins or blueberry greek yogurt muffins!

Healthy chocolate chip pumpkin muffins on a cooling rack.

Why You’ll Love These Healthy Chocolate Chip Pumpkin Muffins

  • A cross between breakfast and dessert! These muffins are slightly sweet with gooey chocolate but still nutritious!
  • Gluten-free and dairy-free + great for meal prep
  • A healthier alternative to traditional muffins that will leave you feeling energized (and without the sugar crash)
  • Ready to eat in just 30 minutes!
  • The perfect lightened-up fall treat to bake up that’s so easy! It will make the whole house smell like baked pumpkin pie!

Ingredients and Substitutions

Ingredients for healthy chocolate chip pumpkin muffins.
  • Pumpkin puree – Libby’s has the best orange color and pumpkin flavor! Make sure to get get pumpkin puree, not pumpkin pie filling
  • Unsweetened applesauce – you can sub with mashed banana
  • Pure maple syrup – can also use honey or substitute for sugar-free pancake syrup if you want less sugar!
  • Coconut oil – melted butter or oil of choice
  • Eggs
  • Vanilla
  • Oat flour – all-purpose flour (GF if needed) or white whole wheat flour work too
  • Pumpkin pie spice – store-bought or homemade
  • Baking essentials: baking powder, salt, and baking soda
  • Mini chocolate chips

How To Make

The full printable recipe is below, but let me walk you through the process so you know what to expect when you’re making it!

Wet ingredients for healthy chocolate chip pumpkin muffins in a bowl.

1. In a large mixing bowl, mix together the pumpkin, applesauce, maple syrup, coconut oil, eggs and vanilla. 

Dry ingredients for healthy chocolate chip pumpkin muffins in bowl.

2. In a small bowl, whisk together the flour, pumpkin pie spice, baking powder, salt and baking soda. 

Ingredients for healthy chocolate chip pumpkin muffins in a mixing bowl with a wooden spoon.

3. Add the dry ingredients to the wet ingredients and mix until combined.

Chocolate chips being added to the batter in the mixing bowl with a wooden spoon.

4. Fold in the chocolate chips. 

Healthy chocolate chip pumpkin muffins in a muffin pan before being baked.

5. Scoop batter to a greased muffin pan. Top with extra chocolate chips so they’re pretty!

Healthy chocolate chip pumpkin muffins in a muffin pan after being baked.

6. Bake for 20-22 minutes at 350F, or until a toothpick inserted comes out mostly clean.

How To Store

Store leftover muffins in an airtight container in the fridge for up to a week. 

To freeze, allow muffins to cool completely then wrap muffins tightly in a freezer-safe bag and freeze for up to 3 months. 

Baking Tips!

  • Don’t over mix. Over mixing the batter can cause denser muffins (instead of light and fluffy) muffins like we all love! For the best results, mix until ingredients are just combined then fold in the blueberries.
  • Check baking soda and baking powder. Ensure they haven’t been open for more than 3 months. I like to write the date on top of the can whenever I open a new one to ensure I know when to start fresh!
  • Don’t overfill muffin tin. Fill only about 3/4 full or the muffin tops will rise too much and fall to the sides!
Healthy chocolate chip pumpkin muffins on a cooling rack.

FAQ: Healthy Chocolate Chip Pumpkin Muffins

Can I use another flour instead of oat flour?

The oat flour really brings an incredible texture to these muffins that is so good! But you could also use an all-purpose flour, white whole wheat flour, or a 1:1 gluten-free flour.

What’s the best kind of pumpkin to use for this healthy pumpkin muffin recipe?

I always recommend using Libby 100% pure pumpkin for any of my pumpkin treats! I think Libby has the best color, taste and texture. Also be sure you’re using pumpkin puree (where the only ingredient is pumpkin) not pumpkin pie filling. 

Can I bake this chocolate chip pumpkin muffin recipe in a loaf pan instead of regular pumpkin muffins?

Sure! You can easily use a loaf pan to make a healthy, quick pumpkin bread. Just be sure to adjust the baking time as it will take longer for the bread to bake. You can check the bread with a toothpick and it’s done once the toothpick comes out mostly clean (the bread will finish baking in the hot pan once removed from the oven). 

How do these muffins stay moist without butter or vegetable oil?

The combination of pumpkin and the unsweetened applesauce pair perfectly to make these muffins light and moist! They also help lightened up this recipe since we aren’t using butter which is high in fat and calories. Not only does the pumpkin help this recipe be lower in calories but you get the added benefits of pumpkin being a vegetable so there is added fiber, vitamins, minerals and antioxidants! 

More Pumpkin Recipes You’ll Love For Pumpkin Season

Pumpkin chocolate chip protein french toast bake on a small plate being drizzled with maple syrup.

Pumpkin Chocolate Chip Protein French Toast Bake

Pumpkin Cinnamon rolls topped with icing in a baking dish.

Healthy Pumpkin Cinnamon Rolls (That Taste Like the Real Deal)

Creamy pumpkin pie protein overnight oats served in jars topped with whipped cream and pecans, garnished with a cinnamon stick.

High Protein Pumpkin Overnight Oats

Pumpkin Baked Oatmeal topped with Vanilla Maple Cream Cheese Frosting on a small plate with a fork.

The Most Bomb Healthy Pumpkin Oatmeal Bake

Did you make this? If you snap a photo, please be sure leave a review, tag me on Instagram or TikTok at @LaurenFitFoodie or hashtag #LaurenFitFoodie so I can see your creations!

Healthy chocolate chip pumpkin muffins on a cooling rack.
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5 from 10 votes

Healthy Chocolate Chip Pumpkin Muffins

? Dairy-Free ? Gluten-Free ? Macro-friendly ? Vegetarian
These Healthy Chocolate Chip Pumpkin Muffins have the best tender, fluffy muffins pumpkin base with gooey chocolate all throughout! They're nutritious and seriously great for breakfast, snack or dessert. Even better, they couldn't be easier to make and are ready in just 30 minutes!
Yield: 12
Prep: 10 minutes mins
Cook: 20 minutes mins
Total: 30 minutes mins
Calories: 194kcal
Protein: 4.3g
Fat: 8.5g
Carbs: 25.1g

Ingredients

  • 1 cup pumpkin puree (240g) Libby’s has the best orange color!
  • 1/4 cup unsweetened applesauce (60g) or mashed banana
  • 1/4 cup pure maple syrup (60g)
  • 1/4 cup coconut oil (60g) melted
  • 2 large eggs
  • 1 tsp vanilla extract
  • 2 cups oat flour (240g)
  • 1 Tbsp pumpkin pie spice
  • 1.5 tsp baking powder
  • 1/2 tsp salt and baking soda each
  • 1/3 cup mini chocolate chips

Before You Begin! If you make this, please leave a review and rating letting us know how you liked this recipe! This helps our business thrive & continue providing free recipes. Scroll for macros and MyFitnessPal code.

Instructions

  • Preheat the oven to 350 degrees F. Grease a muffin pan with cooking oil and/or line with liners.
  • In a large bowl, mix together the pumpkin, applesauce, maple syrup, coconut oil, eggs and vanilla.
  • In a small bowl, whisk together the flour, pumpkin pie spice, baking powder, salt and baking soda.
  • Add the dry ingredients and chocolate chips to the wet ingredients. Fold just until the dry ingredients are incorporated and you see no more streaks of flour.
  • Scoop batter into the greased muffin pan. Sprinkle a few extra chocolate chips on top if desired (so they’re pretty!)
  • Bake for 20-22 minutes, or until a toothpick inserted comes out mostly clean. Let cool for 10 minutes then enjoy!

Equipment

  • Muffin pan

Nutrition Information

Serving: 1muffin, Calories: 194kcal (10%), Carbohydrates: 25.1g (8%), Protein: 4.3g (9%), Fat: 8.5g (13%), Saturated Fat: 2g (13%), Fiber: 1.9g (8%), Sugar: 8.5g (9%)

Nutrition is hand-calculated and accurate. No autocalulations! However, note that values can vary based on the brands you use and if you substitute ingredients.

MyFitnessPal Entry

LFF Healthy Chocolate Chip Pumpkin Muffins

© Author: Lauren

Healthy chocolate chip pumpkin muffins on a cooling rack.

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Lauren

Lauren lives with her husband, Simon and two dogs, Finley and Cookie, in the Carolina’s. She has college degrees in Nursing and Exercise Science, is a NASM certified trainer and spent many years as a macro coach before transitioning to full time blogging. She loves staying active, being creative and recreating her favorite comfort food dishes into healthier, lightened up versions. Desserts are her speciality!

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I’m Lauren, a food lover sharing healthy, macro-friendly recipes that taste good and you can feel good about eating. Here you’ll find everything from breakfasts to easy dinners to lightened up desserts because desserts are absolutely mandatory around here!

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