These Healthy Pumpkin Muffins are made with oat flour and are loaded with warming fall spices. They’re healthier than your average muffin while still being soft, fluffy and tasty. These muffins can be made directly in a bowl and are perfect to enjoy for breakfast or a snack!

a pumpkin muffin with a bite taken out of it

Healthy pumpkin chocolate chip muffins

I love when I can put a healthier spin on a baked good recipe but still have it taste delicious. This recipe for Healthy pumpkin muffins with chocolate chips is healthier than your average pumpkin muffin recipe. These muffins are made with oat flour, and avocado oil and are sweetened with maple syrup for a heathy-ish muffin that doesn’t sacrifice taste!

These muffins have similar ingredients to my Healthy Pumpkin Bread and Healthy Chocolate Pumpkin Bread but are made with oat flour for a healthier twist. These muffins are also loaded with dark chocolate chips to give them that chocolatey flavour in every bite.

Enjoy these Healthy Pumpkin Chocolate Chip Muffins for a breakfast on the go, an afternoon snack with a cup of tea, or a little dessert in the evening.

Why you’ll love these pumpkin muffins with oat flour

  • All the best Fall flavours. These muffins combine flavours like vanilla, pumpkin spice, pumpkin puree and chocolate which results in a really decadent muffin that tastes like it was meant for fall!
  • Versatile and customizable. These muffins are versatile and can be made with oat flour, (as the recipe calls for) all-purpose flour or a 1-1 gluten-free flour blend. You can also add any mix-ins you love to this recipe.
  • Easy to make. This recipe is easy to make and can be whipped up using just 2 bowls and a spatula! No mixers or fancy equipment is needed.

Pumpkin Muffin ingredients and substitutions

  • Oat flour: you can use homemade oat flour which is made by blending oats, or buy oat flour from your local grocery store.
  • Baking powder & baking soda: both of these rising agents are added to the muffins to make them light and fluffy.
  • Salt: just a pinch of salt to balance out the sweetness of the muffins
  • Pumpkin pie spice: you can buy pumpkin pie spice or make your own at home. You can also substitute this ingredient with 1 teaspoon of cinnamon and 1/2 teaspoon of nutmeg if you prefer.
  • Eggs: 2 eggs are used in these muffins. I haven’t tested out this recipe using a flax egg for a vegan version, but I imagine it would work.
  • Maple syrup: to sweeten the muffins and add that perfect Fall flavour. You can also use honey, agave nectar or brown sugar.
  • Avocado oil: this is a healthy oil that has a very neutral taste. You could also use melted butter, coconut oil or canola oil.
  • Almond milk: just a bit to add moisture to the muffins. Any type of milk or even water will work.
  • Pumpkin puree: make sure to use pumpkin puree and not pumpkin pie filling. You can also make homemade pumpkin puree by roasting a pumpkin and blending it.
  • Vanilla extract: use the real stuff for the best taste!
  • Mini chocolate chips: I use dark chocolate mini chocolate chips, but any type of chocolate chips will work!

How to make homemade oat flour

While you can buy store-bought oat flour at most grocery stores, it is cheaper to make oat yourself. (Oh, and did I mention it’s also super easy?)

To make homemade oat flour, just blend some quick oats or rolled oats in a food processor or blender until it’s a fine powder like in the photo below. This process will be easiest if you use quick oats since they are already more processed than rolled oats.

How to make Healthy Pumpkin Muffins

Step 1

Mix the eggs, avocado oil, maple syrup, pumpkin puree and vanilla extract in a bowl. Whisk together until combined.

Step 2

In a separate bowl, mix the oat flour, baking powder, baking soda, salt and pumpkin pie spice together. Then add the dry ingredients to the bowl of wet ingredients and gently mix together to combine.

Step 3

Once the batter is mixed, add in the dark chocolate chips and gently give it another mix to incorporate the chocolate chips into the batter.

Step 4

Line a muffin pan with liners and spray with cooking spray to prevent sticking. Spoon the muffin batter into the moulds filling 3/4 of the way full. Sprinkle more chocolate chips on top. Bake at 350 degrees F for 18-22 minutes or until a toothpick comes out clean.

Pumpkin muffins mix-ins and add-ins

There are so many different mix-ins and add-ins you can add to these pumpkin muffins. I love adding mini chocolate chips so there is some chocolate in every bite, but if you’re not a chocolate chip person, here are some other options:

  • add 1/4 cup of cocoa powder to the batter to make these chocolate pumpkin muffins
  • add 1/2 cup chopped pecans or walnuts
  • add 2 tbsp grated orange zest to the batter
  • add 1/4 cup rolled oats for an oaty bite in the muffins

How to make homemade pumpkin pie spice

You can buy store-bought pumpkin pie spice which is easier to make in this recipe, or even just use a combination of cinnamon and nutmeg to make a delicious muffin.

But if you’d like to make your own pumpkin pie spice, combine 2 tbsp ground cinnamon, 1 tsp ground ginger, 2 tsp ground nutmeg, 1/2 tsp ground allspice and 1/2 tsp ground cloves together. It’s a great spice blend to have on hand for the fall season!

pumpkin muffins in muffin liners on a marble counter

How to store these muffins

Fridge: Store any leftover muffins in a sealed container on the counter for up to 4 days or in the fridge for up to 7 days. If storing in the fridge, you may want to slightly warm the muffins in the microwave before eating.

Freezer: This recipe is also freezer-friendly. To freeze the muffins let them cool completely on the countertop then transfer them to a freezer bag and place them in the freezer for up to 2 months. Defrost on the counter and warm in the oven.

Tips for making Healthy Pumpkin Muffins

  • Make sure to use pumpkin puree and not pumpkin pie filling. The two are not the same! Pumpkin pie filling is sweetened and has a bunch of ingredients added to it. Pumpkin puree should only have one ingredient (pumpkin) on the label.
  • Don’t overmix the batter. This will result in a tougher and less fluffy muffin. It’s ok if there are a few small lumps in the batter.
  • Use a spatula to mix the batter. This will allow you to gently fold the batter together to prevent overmixing.
  • Only fill the muffin tin 3/4 of the way full, otherwise, the muffin batter can overflow.
  • Top the muffins with extra chocolate chips. Not only do they make the muffins look pretty, but you’ll get even more chocolate in every bite!

Pumpkin Muffins FAQ

Can I make these muffins with all-purpose flour?

Yes. If you don’t want to use oat flour you can substitute it with equal parts of all-purpose flour.

How many calories are in homemade pumpkin muffins?

Each one of these muffins has 200 calories, 2 grams of fibre and 4 grams of protein.

Can I make this recipe into a pumpkin loaf?

Yes, if you prefer making a pumpkin loaf instead of pumpkin muffins you can make this recipe in a loaf pan. In this case, you’ll want to bake the pumpkin loaf at 350 degrees for 45-55 minutes or until a toothpick comes out clean.

Can I use pumpkin pie filling instead of pumpkin puree?

No, I wouldn’t recommend it. Pumpkin pie filling is loaded with sugar and other ingredients and will alter the taste of the muffins.

pumpkin muffins topped with chocolate chips

More pumpkin recipes to try

If you tried these Healthy Pumpkin Chocolate Chip Muffins or any other recipe on the blog let me know how you liked it by leaving a comment/rating below! Be sure to follow along on PinterestInstagram and Facebook for even more deliciousness!

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a pumpkin muffin with a bite taken out of it

Healthy Pumpkin Muffins

  • Author: Jessica Hoffman
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert, Breakfast
  • Method: Bake
  • Cuisine: American
  • Diet: Vegetarian


The perfect fall muffin loaded with pumpkin, pumpkin spice and chocolate chips!


Units Scale


  1. Preheat the oven to 350 degrees F, line a muffin pan with muffin liners.
  2. Mix the oat flour, baking powder, baking soda, salt and pumpkin pie spice together in a bowl.
  3. In a separate bowl mix together the eggs, maple syrup, avocado oil, almond milk, pumpkin pureé and vanilla extract.
  4. Pour the dry ingredients into the bowl of wet ingredients and gently fold them together to combine.
  5. Add the chocolate chips and stir together again.
  6. Spoon the batter into the muffin pan filling each mould 3/4 of the way full. Top with more chocolate chips if you like.
  7. Bake for 18-22 minutes or until a toothpick comes out clean. 
  8. Let the muffins cool before eating. 


You can buy oat flour or make it yourself by blending oats in a food processor or blender until it’s a fine powder. You can also substitute the oat flour with 1 1/2 cups of all-purpose flour. 

No pumpkin pie spice? Use 1 tsp of cinnamon and 1/2 tsp of nutmeg


  • Serving Size: 1 muffin
  • Calories: 200
  • Sugar: 12g
  • Sodium: 160mg
  • Fat: 11g
  • Saturated Fat: 3g
  • Carbohydrates: 21g
  • Fiber: 2g
  • Protein: 4g

Keywords: healthy pumpkin muffins, pumpkin muffins with chocolate chips, chocolate chip pumpkin muffins healthy