Pumpkin Chocolate Chip Muffins: Easy, Healthy Fall Recipe

If you’re looking for a quick and wholesome treat that captures the cozy flavors of fall, these Pumpkin Chocolate Chip Muffins are the answer. Made with creamy peanut butter, pumpkin puree, and naturally sweetened with maple syrup or honey, these muffins are soft, moist, and perfectly spiced.

Unlike traditional muffins loaded with refined flour and sugar, this recipe uses nut butter and pumpkin puree to create a moist base that’s naturally gluten-free and protein-rich. Add in some mini chocolate chips, and you’ve got the ultimate bite-sized snack that works for breakfast, lunch boxes, or a sweet afternoon pick-me-up.

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Mini Pumpkin Chocolate Chip Muffins served with coffee

Pumpkin Chocolate Chip Muffins

These mini Pumpkin Chocolate Chip Muffins are soft, moist, and packed with pumpkin flavor. Sweetened with maple syrup and dotted with melty chocolate chips, they make the perfect fall snack or breakfast treat.
Prep Time 3 minutes
Cook Time 17 minutes
Cooling Time 15 minutes
Total Time 20 minutes
Servings: 20 mini muffins
Course: Breakfast, Dessert, Snack
Cuisine: American
Calories: 120

Ingredients
  

  • 0.75 cup pumpkin puree
  • 1 cup peanut butter (all natural)
  • 0.33 cup maple syrup (or honey)
  • 1 egg
  • 1 tsp baking soda
  • 1 tsp pumpkin spice (or cinnamon)
  • 0.25 tsp salt
  • 0.5 cup mini chocolate chips (+ more for tops of muffins)

Equipment

  • Mini Muffin Tray
  • Wire Rack
  • Large mixing bowl
  • Cookie Scoop
  • Oven

Method
 

  1. Preheat oven to 325°F (160°C). Spray a mini muffin tray with coconut oil.
  2. In a large bowl, mix together all ingredients until just smooth.
  3. Using a cookie scoop, transfer the batter to the muffin tray, filling each slot almost full. Sprinkle extra chocolate chips on top if desired.
  4. Bake for 17 minutes, or until a toothpick comes out clean. For regular-sized muffins, bake 20–22 minutes.
  5. Allow to cool in the tray for at least 15 minutes, then carefully remove and transfer to a wire rack to cool for another 15 minutes.

Notes

These muffins are naturally gluten-free if using certified gluten-free peanut butter and chocolate chips. Store in an airtight container for up to 5 days, or freeze for longer storage.

Why You’ll Love Pumpkin Chocolate Chip Muffins

  • Naturally Gluten-Free  These muffins are made without flour, relying on peanut butter and pumpkin for structure.
  • High in Protein  Peanut butter and egg boost the protein content, making them more filling than typical muffins.
  • Quick & Easy  With just one mixing bowl and a mini muffin tray, you’ll have muffins ready in under 20 minutes.
  • Kid-Friendly  The mini size makes them perfect for lunch boxes or after-school snacks.
  • Fall-Inspired Flavor  Pumpkin spice adds warmth, while chocolate chips provide sweetness in every bite.

Equipment You’ll Need

EquipmentPurpose
Mini muffin trayFor baking 20 bite-sized muffins
Wire rackTo cool muffins evenly
Large mixing bowlTo mix all ingredients together

Ingredients for flourless pumpkin muffins

  • 3/4 cup pumpkin puree (adds moisture and natural sweetness)
  • 1 cup natural peanut butter (provides protein and healthy fats)
  • 1/3 cup maple syrup or honey (natural sweetener)
  • 1 egg (helps bind the muffins)
  • 1 tsp baking soda (leavening agent for rise)
  • 1 tsp pumpkin spice or cinnamon (adds cozy fall flavor)
  • 1/4 tsp salt (balances the sweetness)
  • 1/2 cup mini chocolate chips (+ extra for topping)
Ingredients for Pumpkin Chocolate Chip Muffins

How to make healthy pumpkin muffins Step-by-Step

  1. Preheat the oven to 325℉ (163℃). Lightly spray your mini muffin tray with coconut oil or use muffin liners.
  2. In a large mixing bowl, combine pumpkin puree, peanut butter, maple syrup (or honey), egg, baking soda, pumpkin spice, and salt. Stir until smooth but avoid overmixing.
  3. Fold in the mini chocolate chips until evenly distributed.
  4. Using a cookie scoop or spoon, transfer batter into the mini muffin tray, filling each slot nearly full.
  5. Sprinkle a few extra chocolate chips on top for a bakery-style finish.
  6. Bake for 17 minutes, or until a toothpick inserted into the center comes out clean.
    • If baking regular-sized muffins, increase the time to 20–22 minutes.
  7. Allow muffins to cool in the tray for at least 15 minutes to set, then carefully remove and place on a wire rack for another 15 minutes before serving.
Scooping batter for Pumpkin Chocolate Chip Muffins

Nutrition Benefits (Per mini pumpkin muffin – Approx. 20 muffins)

NutrientAmountBenefit
Calories~95 kcalLight but satisfying
Protein3 gBoost from peanut butter and egg
Carbohydrates9 gNatural energy from pumpkin & maple syrup
Fiber2 gSupports digestion
Fat5 gHealthy fats from peanut butter
Sugar5 gNaturally sweetened, balanced by pumpkin

Variations

  • Nut-Free Option  Replace peanut butter with sunflower seed butter or almond butter.
  • Vegan Version  Use a flax egg (1 tbsp ground flaxseed + 3 tbsp water) instead of egg.
  • Double Chocolate  Mix 1 tbsp cocoa powder into the batter for richer flavor.
  • Spiced Up  Add ground ginger or nutmeg for extra warmth.

Serving Suggestions

  • Enjoy warm with a drizzle of honey or maple syrup.
  • Pack into lunch boxes for a kid-approved snack.
  • Pair with coffee or chai for a cozy fall breakfast.
  • Serve alongside Greek yogurt for a balanced, protein-packed snack.
Mini Pumpkin Chocolate Chip Muffins served with coffee

Storage Tips

  • Room Temp: Store in an airtight container up to 2 days.
  • Fridge: Lasts 5–6 days when refrigerated.
  • Freezer: Freeze muffins individually for up to 2 months. Defrost at room temp or microwave for 15–20 seconds.

FAQs About Pumpkin Chocolate Chip Muffins

Can I make these with almond butter?

Yes, almond butter works just as well as peanut butter.

Can I use fresh pumpkin puree?

Absolutely! Just make sure it’s thick and not watery.

Are these muffins gluten-free?

Yes, since they don’t contain flour, they’re naturally gluten-free.

Can I make them without chocolate chips?

Of course add raisins, cranberries, or nuts instead.

How do I keep them moist?

Don’t over bake and store in an airtight container.

Can I make these as full-size muffins?

Yes, just adjust the baking time to about 20–22 minutes.

Conclusion

These Pumpkin Chocolate Chip Muffins are the perfect combination of cozy pumpkin spice and sweet chocolate in a mini, bite-sized package. They’re quick to make, naturally gluten-free, and full of wholesome ingredients making them a family-friendly snack you can feel good about.

Whether you bake them for a fall brunch, pack them for school lunches, or enjoy them with your morning coffee, they’ll quickly become a favorite at Flash Meals Club.

For more pumpkin-inspired bakes, check out our Pumpkin Chocolate Chunk Cake or our Pumpkin Cottage Cheese Cheesecake.

Follow Kenz Recipes on Facebook for more delicious ideas, behind-the-scenes baking, and quick meal tips.

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