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Healthy Chocolate Pumpkin Muffins: An Easy Fall Treat

What if you could start your day with a treat that feels indulgent but is secretly packed with wholesome goodness? During the cozy autumn months, the craving for something warm, spiced, and chocolatey is real. That’s where these incredible Feel-Good Chocolate Pumpkin Muffins come in. They are delightfully moist, perfectly spiced, and studded with pockets of melted chocolate, all while being made with nutritious ingredients like pumpkin puree and whole wheat flour. This is the ultimate fall recipe for a quick breakfast, a healthy snack, or a guilt-free dessert that the whole family will adore.

Ingredients for Your Muffins

This recipe uses simple, wholesome ingredients to create incredibly moist and flavorful muffins.

IngredientAmount/Quantity
Thick pumpkin puree (like Libby’s)1 cup*
Large eggs2
Avocado oil or other neutral oil⅓ cup
Pure maple syrup⅓ cup
Pure vanilla extract2 teaspoons
Fine sea salt½ teaspoon
Baking soda½ teaspoon
Baking powder1 teaspoon
Unsweetened cocoa powder¼ cup
White whole wheat flour**¾ cup
Mini chocolate chips⅓ cup

*Note on puree: If your pumpkin puree is thin (applesauce consistency), reduce the amount to ¾ cup.
**Note on flour: Regular whole wheat, all-purpose, or a 1-to-1 gluten-free flour blend will also work perfectly.

Timing

These delicious muffins come together in a flash, making them perfect for a quick baking session.

  • Preparation Time: 15 minutes
  • Cooking Time: 20 minutes
  • Total Time: 35 minutes

Step-by-Step Instructions

Follow these simple steps to bake a perfect batch of chocolate pumpkin muffins.

Step 1: Preheat Oven and Prep Muffin Pan

First things first, let’s get your kitchen ready. Preheat your oven to 350°F (175°C). While the oven heats up, line a standard 12-cup muffin pan with paper liners. Using liners prevents sticking and makes cleanup a breeze.

Step 2: Whisk the Wet Ingredients

In a large mixing bowl, whisk together the eggs, pumpkin puree, oil, maple syrup, and vanilla extract until smooth and well combined. Next, whisk in the leavening agents and salt—the salt, baking powder, and baking soda—until they are fully incorporated into the wet mixture.

Step 3: Fold in the Dry Ingredients

Now, switch from a whisk to a spatula or a large spoon. Add the cocoa powder, flour, and mini chocolate chips to the bowl. Gently fold the dry ingredients into the wet until everything is just combined. Tip: Be careful not to overmix! A few lumps in the batter are perfectly fine and are the secret to tender, fluffy muffins.

Step 4: Fill Muffin Cups and Bake

Using a scant ¼ cup measuring cup or a large cookie scoop, evenly divide the batter among the 12 prepared muffin cups. This ensures all your muffins are the same size and bake evenly. Place the pan in the preheated oven and bake for 18-20 minutes. You’ll know they’re done when a toothpick inserted into the center of a muffin comes out clean.

Step 5: Cool and Enjoy

Once baked, remove the muffins from the oven and let them cool in the pan for a few minutes before transferring them to a wire rack to cool completely. While they’re delicious warm with gooey chocolate chips, letting them cool helps them set up perfectly.

Nutritional Information

Here is an estimated nutritional breakdown per muffin (assuming a batch of 12). Please note this is an approximation.

  • Calories: 165 kcal
  • Protein: 3 g
  • Fat: 9 g (Saturated: 2 g)
  • Carbohydrates: 20 g (Fiber: 3 g, Sugar: 10 g)

These muffins are a great source of Vitamin A from the pumpkin and provide a good dose of fiber from the whole wheat flour.

Healthier Alternatives

While this recipe is already quite healthy, here are a few ways to customize it for your dietary needs.

  • Make it Vegan: Replace the two eggs with two “flax eggs” (2 tablespoons of ground flaxseed mixed with 5 tablespoons of water).
  • Make it Gluten-Free: As noted in the ingredients, you can easily swap the whole wheat flour for your favorite 1-to-1 gluten-free baking blend.
  • Add a Nutrient Boost: Stir in a tablespoon of chia seeds or ground flaxseed along with the dry ingredients for extra fiber and omega-3s.

Serving Suggestions

These Chocolate Pumpkin Muffins are wonderfully versatile and perfect for any time of day!

  • Quick Breakfast: Grab one or two on your way out the door for a delicious and satisfying breakfast on the go.
  • Afternoon Snack: Pair a muffin with a hot cup of coffee or tea for the perfect afternoon pick-me-up.
  • Healthy Dessert: Warm a muffin slightly and top it with a smear of peanut butter, almond butter, or a dollop of Greek yogurt for a wholesome dessert.

Common Mistakes to Avoid

Keep these simple tips in mind to ensure your muffins turn out perfectly every time.

  • Overmixing the Batter: This is the most common muffin mistake. Overmixing develops the gluten in the flour, resulting in tough, dense muffins instead of light, tender ones. Solution: Mix only until the flour is no longer visible. Stop stirring as soon as the ingredients are combined.
  • Using Watery Pumpkin Puree: The consistency of pumpkin puree can vary by brand. A thin, watery puree can make the batter too wet. Solution: Use a thick puree like Libby’s. If yours seems thin, reduce the amount to ¾ cup or blot it with a paper towel to absorb excess moisture before measuring.
  • Overbaking: Even an extra minute or two in the oven can turn a moist muffin into a dry one. Solution: Start checking for doneness at the 18-minute mark. As soon as a toothpick comes out clean, they’re ready!

Storing Tips

These muffins store wonderfully, making them great for meal prep.

  • Room Temperature: Muffins can be stored in an airtight container at room temperature for up to 24 hours.
  • Refrigerator: For longer freshness, store them in an airtight container in the fridge for up to 5 days.
  • Freezer: These muffins freeze beautifully! Wrap each muffin individually in plastic wrap and then place them in a freezer-safe bag or container. They will keep for up to a month. Simply thaw at room temperature or gently warm in the microwave.

Conclusion

These Feel-Good Chocolate Pumpkin Muffins are the perfect embodiment of fall baking: cozy, delicious, and made with wholesome ingredients you can feel good about. They are incredibly easy to whip up and are sure to become a seasonal staple in your kitchen. Whether for a busy morning, a school lunchbox, or a simple treat, this recipe delivers on both flavor and nutrition. We hope you enjoy every last bite! Try the recipe and let us know how you liked it in the comments below. We’d love to hear from you!

FAQs

Q1. Can I use a different type of flour?

Yes! The recipe is very forgiving. You can use regular all-purpose flour, whole wheat flour, or a 1-to-1 gluten-free baking flour blend with great results.

Q2. Can I make these muffins without the chocolate chips?

Absolutely. If you prefer, you can omit the chocolate chips entirely or swap them for chopped nuts (like pecans or walnuts), raisins, or dried cranberries for a different twist.

Q3. Can I use a different sweetener instead of maple syrup?

Honey or agave nectar would work well as a substitute for maple syrup in the same quantity. Keep in mind that this will slightly alter the flavor.

Q4. How do I know if my pumpkin puree is thick enough?

A thick puree will be dense and almost hold its shape on a spoon, similar to the consistency of hummus. A thin puree will be looser and more watery, closer to the consistency of applesauce. If you turn the spoon upside down and it slides right off, it’s likely too thin.

Healthy Chocolate Pumpkin Muffins: An Easy Fall Treat

Evelyn Marcella Rivera
Moist, chocolatey, and pumpkin-packed muffins made with wholesome ingredients. Perfect for cozy fall mornings or a quick snack—no mixer needed!
Prep Time 15 minutes
Cook Time 20 minutes
Cooling Time 10 minutes
Total Time 35 minutes
Course Breakfast, Dessert, Snack
Cuisine American
Servings 12 muffins
Calories 165 kcal

Equipment

  • 12-cup muffin pan
  • Paper muffin liners
  • Mixing bowl (large)
  • Mixing bowl (medium)
  • Whisk
  • Spatula or large spoon
  • Measuring Cups & Spoons
  • Cookie scoop or 1/4 cup measure
  • Wire rack

Ingredients
  

Muffins

  • 1 cup thick pumpkin puree (like Libby’s) use 3/4 cup if puree is thin
  • 2 large eggs
  • 1/3 cup avocado oil or other neutral oil
  • 1/3 cup pure maple syrup
  • 2 tsp pure vanilla extract
  • 1/2 tsp fine sea salt
  • 1/2 tsp baking soda
  • 1 tsp baking powder
  • 1/4 cup unsweetened cocoa powder
  • 3/4 cup white whole wheat flour or regular whole wheat, all-purpose, or 1:1 gluten-free blend
  • 1/3 cup mini chocolate chips

Instructions
 

  • Preheat Oven and Prep Muffin Pan: Preheat the oven to 350°F (175°C). Line a standard 12-cup muffin pan with paper liners.
  • Whisk the Wet Ingredients: In a large bowl, whisk together the eggs, pumpkin puree, oil, maple syrup, and vanilla until smooth. Whisk in the salt, baking powder, and baking soda until fully incorporated.
  • Fold in the Dry Ingredients: Switch to a spatula. Add the cocoa powder, flour, and mini chocolate chips. Gently fold until just combined—a few small lumps are okay.
  • Fill Muffin Cups and Bake: Divide the batter evenly among the 12 cups (about scant 1/4 cup each). Bake 18–20 minutes, or until a toothpick in the center comes out clean.
  • Cool and Enjoy: Cool in pan for a few minutes, then transfer to a wire rack to cool completely before serving.

Notes

Storage: Keep at room temperature in an airtight container for up to 2 days, or refrigerate up to 5 days. Freeze up to 2 months. If your pumpkin puree is thin, use 3/4 cup.
Keyword fall treat, healthy chocolate pumpkin muffins, muffin recipe