Name: Healthy Pumpkin Muffins
Prep time: 10 min
Cook time: 25 min
Total time: 35 min
Cuisine: American
Ingredients: 2 cups flour, all-purpose; 1 teaspoon baking powder; 1/2 teaspoon baking soda; 1/2 teaspoon salt; 2 teaspoons cinnamon; 1 teaspoon ginger; 1/2 teaspoon nutmeg; 1/2 teaspoon cloves; 1 cup pumpkin purée; 2 eggs; 1/2 cup milk; 1/3 cup butter, melted, plus more for greasing; 1/2 cup maple syrup; 2 tablespoons molasses; 1 teaspoon vanilla extract

Naturally sweetened and high in fiber, these healthy pumpkin muffins are a delicious treat with all of the flavors of fall. They work well as a healthy snack or on-the-go breakfast, just be sure to make a double batch because they are so tasty they won’t last long.

Healthy pumpkin muffins on a cooling rack with a pitcher of milk and a tea towel in the background.

There is a misconception that all muffins are unhealthy, but I need you to know, that is not the case. In truth, muffins can be both a healthy choice and an unhealthy choice, it all depends on the ingredients that they were made with!

When loaded with vegetable oils, refined flour, and refined sugar, they are certainly a less-than-ideal choice, but when made with real food any muffin has a place in a healthy diet, and that’s exactly what these healthy pumpkin muffins are.

Healthy pumpkin muffin cut in half with butter on top on a white plate with a glass of milk in the background.

Why You’ll Love These Healthy Pumpkin Muffins

Quick & Easy – Ready in under 30 minutes, these pumpkin muffins are very quick to prepare.
Light & Fluffy – These muffins are incredibly moist.
Full of Flavor – Filled with a mixture of pumpkin pie spices, these muffins are equally delicious as they are nutritious.
Versatile – These healthy pumpkin muffins work well for snacks, breakfasts, or desserts.

Ingredients for Healthy Pumpkin Muffins

Flour – The recipe calls for all-purpose flour, however, you could use whole wheat flour or 1-to-1 gluten-free flour if preferred.
Pumpkin Purée – To add moisture and pumpkin flavor. You can use canned pumpkin purée and homemade pumpkin purée, both with work. If using canned, just be sure not to use pure pumpkin and not pumpkin pie filling.
Pumpkin Pie Spice – A mix of cinnamon, nutmeg, ginger, and cloves to add a hint of pumpkin spice flavor.
Maple Syrup – To sweeten the muffins and add flavor. While pure maple syrup is recommended, you can use brown sugar if you prefer.
Molasses – To add moisture and enhance the flavor.
Eggs – To add structure and ensure the muffins are light and fluffy.
Milk – You can use whole milk, 2% milk, skim milk, or non-dairy milk of your choice in these pumpkin muffins.
Butter – To ensure the muffins are moist. While unsalted butter is recommended, salted and unsalted will work.
Vanilla Extract – To enhance the sweetness.
Baking Essentials – Some baking powder, baking soda, and salt to ensure the muffins are light and fluffy.

Flour, baking soda, baking powder, salt, and pumpkin pie spice in a white mixing bowl.

Dry ingredients for healthy pumpkin muffins in a white mixing bowl.

Dietary Adaptions

To Make them Gluten-Free: Swap the all-purpose flour for 1-to-1 gluten-free flour.

To Make them Dairy-Free: Swap the milk for almond milk and butter for coconut oil or olive oil.

To Make them Egg-Free: Swap the eggs for 2 flax eggs.

Pumpkin puree, maple syrup, molasses, melted butter, eggs, and vanilla in a large mixing bowl.

Wet ingredients for healthy pumpkin muffins in a large mixing bowl.

How to Make Healthy Pumpkin Muffins

Mix the dry ingredients. In a medium mixing bowl, add the flour, baking powder, baking soda, salt, pumpkin spice mix, and stir to combine.
Mix the wet ingredients. In a large bowl, add the pumpkin purée, maple syrup, molasses, eggs, melted butter, milk, and vanilla extract, and stir until well combined.
Mix the batter. Add the dry ingredients to the wet ingredients and fold until combined.
Add to a muffin pan. Divide the muffin batter evenly across muffin cups.
Bake until golden and fluffy. Transfer the muffins to the oven and bake at 350°F for 22-25 minutes or until a toothpick inserted comes out clean.
Serve and enjoy!

You can find the detailed instructions in the recipe card below.

Wet ingredients and dry ingredients for healthy pumpkin muffins in large mixing bowl.

Batter for healthy pumpkin muffins in a large mixing bowl.

Red’s Nutrition Tip

To make these healthy pumpkin muffins a more balanced meal or snack, serve them with a source of protein such as Greek yogurt, skyr, cottage cheese, cheddar cheese, or a drizzle of almond butter.

Tips for the Best Healthy Pumpkin Muffins

Make your own pumpkin purée. While you can certainly use canned pumpkin purée for this recipe, homemade pumpkin purée is very easy to make and much more cost-effective. Simply seed a sugar pumpkin, cut it into wedges, add it to a baking dish or baking sheet, and roast it in the oven at 400°F until tender. Once roasted, remove the skin and purée the flesh in a blender until smooth.
Add oats. Add extra fiber to the batter by swapping 1/2 cup of the flour for 1/2 cup of old-fashioned rolled oats.
Mix them up. Add additional flavor and texture to these healthy pumpkin muffins by adding chocolate chips, chopped nuts, or dried fruit to the batter. See details below.

Optional Add-Ins

These muffins are great on their own, but if you’d like to make them extra special, you can add one of the following, or a combination of the following, to the pumpkin muffin batter:

1 cup chopped dark chocolate
1 cup mini chocolate chips
1 cup chopped walnuts
1 cup chopped pecans
1 cup pumpkin seeds
1 cup dried cranberries
1 cup chopped dates
1 cup raisins

Storage + Reheating

To Store: Allow the pumpkin muffins to cool and then place them in an airtight container and store them at room temperature for up to 4 days or in the refrigerator for up to 6 days.

To Freeze: Allow the muffins to cool completely and then place them in a single layer in a freezer bag and store them in the freezer for up to 3 months.

To Reheat: To thaw frozen muffins, allow them to thaw at room temperature, or use a thaw setting on your microwave. Once thawed, you can warm them in the microwave for 30 seconds, or in the oven at 350°F wrapped in aluminum foil for 5-10 minutes.

More Healthy Pumpkin Recipes: