My healthy pumpkin muffins are lightened up with less fat and sugar, but are every bit as moist and fluffy as you’d expect. They are quick and easy to make and perfect for a wholesome snack or afternoon treat.

Come fall, my healthy pumpkin muffin recipe becomes an almost weekly staple in my household. It’s the perfect use of pumpkin puree, uses wholesome ingredients, and is one of the few muffins my family begs me to make all the time.

When I was developing these (inspired by my healthy pumpkin bread), I tested them head-to-head with my classic pumpkin muffin recipe I showcased in culinary school (the kind loaded with butter and SO much sugar). Instead of white sugar, I like to use a little coconut sugar, which is less refined and keeps the muffins low sugar. I also swap out the white flour for oat flour, which adds extra protein, fiber, and whole grains. You could technically call these low-calorie pumpkin muffins, because each giant muffin has less than 150 calories – win!

Table of Contents

1. Key Ingredients
2. How to make healthy pumpkin muffins
3. Arman’s recipe tips
4. Storage instructions
5. Frequently asked questions
6. Healthy Pumpkin Muffins (Recipe Card)
7. More healthy muffin recipes

Why make my healthy pumpkin muffins

• Perfect texture and flavor. The texture is moist and fluffy in the middle with a tender crumb. They are full of pumpkin flavor, thanks to the addition of pumpkin puree to the batter (no pumpkin pie filling!).
• Tastes like bakery muffins. Don’t let the word ‘healthy’ fool you. My muffins taste like any good bakery-style muffin out there!

Key Ingredients

Find the full printable recipe instructions and ingredient quantities below.

• Oat flour. Ground-up rolled or quick oats. Skip the expensive packaged kind and make your own with my homemade oat flour. 
• Baking powder. The leavening agent gives the muffins some rise and fluffiness.
• Pumpkin spice. A must for any recipe using pumpkin puree. You can make your own by mixing ground cinnamon, nutmeg, cloves, and ground ginger. 
• Pumpkin puree. Homemade pumpkin puree or unsweetened canned pumpkin. If you use the latter, be sure that it is NOT pumpkin pie filling.
• Coconut oil. A fantastic alternative to butter. Use refined coconut oil, as it has no coconut flavor whatsoever. You’ll notice that the amount used is much less than in other pumpkin muffins, which helps keep these relatively low-fat yet still moist and fluffy.
• Eggs. room temperature, please.
• Milk of choice. I used unsweetened almond milk to keep them dairy-free, but any milk can be used (such as coconut, soy, or non-fat milk).
• Coconut sugar. A refined sugar-free sweetener. You can find these at Asian grocers or health food stores. Of course, if you only have white or brown sugar, you can use that. I also tested these muffins with maple syrup and honey, and they work well.
• Oatmeal crumb topping. A simple mix of oat flour, rolled oats, sugar, cinnamon, and coconut oil.

How to make healthy pumpkin muffins

Step 1- Make the batter. Whisk together your flour, baking powder, and pumpkin pie spice in a small bowl, then set that aside. In a mixing bowl, whisk together the remaining ingredients until creamy.

Step 2- Combine. Gently fold the dry ingredients into the wet ingredients until fully incorporated, with no air pockets remaining.

Step 3- Make the crumb topping. If desired, make the crumb topping by mixing the oat flour, rolled oats, coconut sugar, cinnamon, and coconut oil.

Step 4- Bake the muffins. Disperse the batter evenly amongst a greased 12-count muffin tin and sprinkle the crumb topping over each one. Bake the muffins for 18-20 minutes or until a skewer comes out mostly clean.

Arman’s recipe tips

• Do not over-bake the muffins. Remember, muffins will continue to bake as they are cooling in the muffin tin. Remove them from the oven when a toothpick comes out mostly clean.
• Use a wire rack. Cool the muffins in the tin for 10 minutes then move them to a wire rack. My first test batch turned soggy on the bottom when I left them in the tin too long.
• Use superfine oat flour. For the best texture of the muffins, the oat flour used must be of a powdery texture. Some brands, like Bob’s Red Mill, are great, but others are a little coarser, so I suggest blending them down even further to a fine powder.
• Adjust the sweetness. These muffins are pleasantly sweet, thanks to the addition of coconut sugar and the natural sweetness of the pumpkin. However, if you prefer a sweeter muffin, add an extra tablespoon or two of coconut sugar.
• Use actual flour. If you prefer muffins made with baking flour, swap out the oat flour with whole wheat flour.

Storage instructions

To store: Muffins can be stored at room temperature, covered, for up to 3 days. If you’d like them to keep longer, store them in the refrigerator and they will keep for up to 1 week.

To freeze: Place muffins in a ziplock bag and store them in the freezer for up to 6 months. Let them thaw completely from their frozen state.

Frequently asked questions

More healthy muffin recipes

• Healthy zucchini muffins
• Healthy blueberry muffins
• Healthy chocolate muffins
• Healthy oatmeal muffins