Pumpkin Chocolate Chip Muffins That Stay Moist and Flavorful

These easy healthy pumpkin chocolate chip muffins are the perfect snack for fall.

pumpkin chocolate chip muffins

These healthy pumpkin chocolate chip muffins taste delicious!

Welcome the cozy flavors of fall with these healthy pumpkin chocolate chip muffins. They’re lightened up using simple, wholesome ingredients while still delivering classic autumn flavor.

Made with plain Greek yogurt, whole wheat flour, rolled oats, and real canned pumpkin puree (not pumpkin pie filling), these muffins are oil-free and come in at under 150 calories each.

pumpkin chocolate chip muffins

Ingredients to make healthy pumpkin chocolate chip muffins

  • Plain Greek yogurt (unsweetened)
  • Pumpkin puree (canned pumpkin, not pumpkin pie filling)
  • Eggs
  • Whole wheat flour
  • Rolled oats (old fashioned)
  • Brown sugar
  • Pumpkin pie spice
  • Vanilla extract
  • Salt
  • Baking soda
  • Baking powder
  • Mini chocolate chips
ingredients to make healthy pumpkin muffins

How to make healthy pumpkin chocolate chip muffins

Step 1: In a medium bowl, whisk together the wet ingredients: 1 cup plain Greek yogurt, 1 cup canned pumpkin puree, 2 eggs, 1/3 cup brown sugar, and 1 tablespoon vanilla extract.

Step 2: In a separate bowl, whisk the dry ingredients: 1 1/4 cups whole wheat flour, 1/2 cup rolled oats, 1 teaspoon pumpkin pie spice, 1/4 teaspoon salt, 1/4 teaspoon baking soda, and 1 teaspoon baking powder.

pumpkin muffins wet ingredients mixed together
dry ingredients for the pumpkin muffins

Step 3: Add the wet ingredients to the dry ingredients and gently mix with a rubber spatula until just combined—do not overmix. Fold in 1/2 cup mini chocolate chips.

wet and dry muffin ingredients mixed together
healthy pumpkin chocolate chip muffin batter in a bowl

Step 4: Line 12 muffin cups with parchment paper liners and evenly distribute the batter between them. Sprinkle extra mini chocolate chips on top for a pretty finish.

Step 5: Bake at 400°F (204°C) for 15–17 minutes, or until a toothpick inserted in the center comes out clean. Cool in the pan briefly, then transfer to a wire rack.

pumpkin muffin batter in lined muffin tins
cooked pumpkin muffin in the muffin tin

How to keep pumpkin muffins from sticking to the liners

Because this recipe contains no added oil, muffins can stick to standard paper liners. Use parchment paper muffin liners or spray regular liners lightly with cooking spray to prevent sticking. Parchment liners work especially well and help muffins release cleanly.

pumpkin chocolate chip muffin in the baking pan

These muffins are moist and fluffy thanks to the Greek yogurt, which also provides protein so they make a satisfying breakfast or a healthier snack. Their lower sugar content keeps them balanced while still satisfying a sweet craving.

pumpkin chocolate chip muffins stacked on top of each other

Enjoy warm from the oven or store leftovers properly for later.

pumpkin chocolate chip muffin in the baking pan

More Pumpkin Recipes

  • Gluten Free Pumpkin Pie Cookies
  • Pumpkin Banana Bread
  • Healthy Pumpkin Truffles
  • Pumpkin Cream Pie
  • No Bake Pumpkin Cheesecake Bars
  • Gluten Free Pumpkin Pie
healthy pumpkin chocolate chip muffins

Pumpkin Chocolate Chip Muffins FAQs

How do I store healthy pumpkin chocolate chip muffins?

Store leftover muffins in an airtight container in the refrigerator for 2–3 days. To freeze, wrap individually and freeze up to 2 months; thaw at room temperature or warm briefly in the microwave.

Can I use another kind of Greek yogurt?

You can use whole-milk plain Greek yogurt if you prefer a richer muffin. Vanilla-flavored yogurt will add sweetness and change the flavor slightly, so reduce the brown sugar if you want a less sweet result.

Is canned pumpkin the same thing as pumpkin pie filling?

No. Canned pumpkin puree contains only pumpkin, while pumpkin pie filling includes added sugar and spices. Use pure pumpkin puree for this recipe.

pumpkin muffin outside of the liner
pumpkin chocolate chip muffins

Healthy Pumpkin Chocolate Chip Muffins

Lightened-up pumpkin muffins with chocolate chips—great for breakfast or a snack.
Prep: 10 mins
Cook: 15 mins
Total: 25 mins
Servings: 12

Ingredients

  • 1 cup plain 0% Greek yogurt
  • 1 cup canned pumpkin puree
  • 2 eggs
  • 1 1/4 cups whole wheat flour
  • 1/2 cup rolled oats
  • 1/3 cup brown sugar
  • 1 teaspoon pumpkin pie spice
  • 1 tablespoon vanilla extract
  • 1/4 teaspoon salt
  • 1/4 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1/2 cup mini chocolate chips

Instructions

  1. Whisk together the wet ingredients: Greek yogurt, pumpkin, eggs, brown sugar, and vanilla.
  2. Whisk together the dry ingredients: whole wheat flour, rolled oats, pumpkin pie spice, salt, baking soda, and baking powder.
  3. Add the wet ingredients to the dry ingredients and stir until just combined. Do not overmix.
  4. Fold in the mini chocolate chips.
  5. Line 12 muffin cups with parchment liners (or spray regular liners). Divide the batter evenly; these make large muffins.
  6. Sprinkle additional mini chocolate chips on top if desired.
  7. Bake at 400°F (204°C) for 15–17 minutes, or until a toothpick inserted comes out clean.

Nutrition

Calories: 148 kcal, Carbohydrates: 25 g, Protein: 5 g, Fat: 3 g, Sugar: 12 g, Fiber: 2 g
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Skinny Pumpkin Chocolate Chip Muffin close up