Healthy Pumpkin Muffin

Transforming my beloved pumpkin muffin recipe, loved by countless families, into these healthy pumpkin muffins meant swapping the vegetable oil for olive oil, incorporating greek yogurt, and using less sugar. This took the recipe from 460 calories per muffin to just about 220 calories, but you would never know because they still taste amazing! 

Healthy Pumpkin Muffins

I always go all in on recipe testing, tweaking until I have a share-worthy final recipe. That’s why I wasn’t worried when I had a few fails while trying to make this recipe healthier. After all, it’s my job to do all of the trial and error so you don’t have to!

For this recipe, I tried some other healthier ingredient swaps and a few batches came out really bad. They were gummy, dense, and not sweet enough. 

Finally, after more tweaking and testing, I found the perfect combination of ingredients to make healthy pumpkin muffins that hit all the marks on flavor, sweetness, and texture.

Coming in at 230 calories less than my traditional pumpkin muffins, I would certainly call that a healthier version!

If you love pumpkin spice during Fall season, you are going to love these delicious muffins. These are great for quick breakfasts, an afternoon snack, or my favorite, the late night snack! Try my recipe once and you’ll see why these are the best healthy pumpkin muffins!

Healthy Pumpkin Muffin Ingredients

Simple, wholesome ingredients come together to make a healthy snack that feels more like a treat, bursting with Fall flavor! Get the full healthy pumpkin muffin recipe with measurements and instructions in the recipe card below. Here is the ingredient list:

• All-purpose flour – properly measured on a kitchen scale.
• Brown sugar – packed!
• Baking powder
• Baking soda
• Salt
• Ground cinnamon
• Ground nutmeg
• Ground ginger
• Pure pumpkin puree – 100% pumpkin puree, not pumpkin pie mix
• Eggs
• Nonfat greek yogurt – I used plain, you could also use vanilla
• Olive oil
• Milk – I used whole milk, you could use skim, 1%, 2%, or almond milk
• Pumpkin seeds, optional 

How to Make Pumpkin Muffins Healthy

Just 5 simple steps to make these easy pumpkin muffins! Keep reading for more tips and the full recipe in the recipe card below. Here are the easy steps:

1. Combine dry ingredients. In a large bowl combine the flour, brown sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger. Stir together and set aside.

2. Combine wet ingredients. In a larger mixing bowl combine the pumpkin, eggs, greek yogurt, olive oil, and milk. Stir to combine.

3. Combine wet and dry ingredients. Gradually mix the dry ingredients into the wet ingredients, mixing just until combined. The batter will be very thick.
4. Rest muffin batter. Cover the bowl with a towel and allow the batter to rest for 15 minutes. During this time, preheat the oven to 425ºF / 220ºC. 

5. Add to pan and bake. For bakery style muffins, line a 12 count muffin tin with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. I recommend spraying the muffin cups with non-stick cooking spray because this batter does tend to stick to the liners. Fill the liners with 6-8 heaping tablespoons of batter. Sprinkle pumpkin seeds over the muffins if desired. Place one muffin pan in the center of the oven and bake for 7 minutes at 425ºF / 220ºC, then keep the muffins in the oven, turn the temperature down to 350ºF / 180ºC and bake for 13-16 minutes or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan. Repeat with the remaining batter, bumping the temperature back up to 425ºF / 220ºC.

Healthy Pumpkin Muffins Recipe Tips

Here are a few tips to make these healthy muffins even better:

• Spray the liners: I recommend spraying the muffin cups with non-stick cooking spray because this batter does tend to stick to the liners.
• Don’t skip the rest time: Allow the batter to rest for 15 minutes in the mixing bowl.
• Create bakery-style domed muffin tops: Filling every other cup allows the muffins to spread and dome without running into each other. This technique also encourages the muffins to brown, creating a golden muffin top.
• Start at a higher temp, then lower: Bake at a higher temperature initially to cause the muffins to rise quickly.
• Properly measure the flour: This is key for the right texture and a tender muffin. Follow the directions below to measure flour correctly.
• Add-ins: ​I like to top these with pumpkin seeds for texture and presentation, but you can also try mixing in chocolate chips if you want to make pumpkin chocolate chip muffins.

Storing and Freezing Muffins

Muffin Storage

If you’ll be eating the muffins within 24 hours of baking, you can leave them uncovered on the counter. The muffins will not dry out while left at room temperature for 1 day. 

In fact, muffins are so moist they can become soggy and those crunchy, sugary tops can disappear when stored in an airtight container.

But I have a trick to help that – paper towels. 

For longer storage, 2-4 days, line the bottom of an airtight container with paper towels. Place the muffins in a single layer in the container then cover the muffins with any additional layer of paper towels. The paper towels will act like a sponge, absorbing the moisture they release while they are stored. 

If the paper towels become too moist around day 2 or day 3, replace them with fresh paper towels. 

How To Freeze Muffins

Individually wrap each muffin in plastic wrap. Then place them in a ziploc bag or airtight container and place in the freezer for up to 3 months.

To thaw, leave them at room temperature until defrosted, about 1 hour. Or unwrap them and microwave at 20 second intervals until defrosted.

More Pumpkin Recipes

• Homemade Pumpkin Pie Recipe
• Pumpkin Patch Cupcakes
• Pumpkin Dump Cake (Easy!)
• No Bake Whipped Cream Pumpkin Pie