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Healthy Pumpkin Muffins

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These Healthy Pumpkin Muffins are made with whole wheat flour, nutrient-packed pumpkin, are lower in sugar, and are loaded with delicious pumpkin spices.

chocolate chip pumpkin muffins in a stack on a white countertop

The Best Pumpkin Muffin Recipe

There are thousands of recipes for pumpkin muffins out there, but after you try this recipe your search will be over. It really is like eating a bakery style muffin and it is perfect for a snack or for an easy on-the-go breakfast. They are moist, not too dense, with just the right amount of sweetness. And yes- they really are healthy, too!!

a muffin tin with chocolate chip pumpkin muffins

Ingredients:

  • flax
  • water
  • flour
  • baking powder
  • baking soda
  • salt
  • spices
  • coconut oil
  • sugar
  • vanilla
  • pumpkin
  • mini chocolate chips
All of the ingredients for pumpkin muffins in individual bowls on a white counter

How to Make Healthy Pumpkin Muffins

This muffin recipe is super easy and one that will quickly become your favorite!

  1. Start by preheating your oven to 375 degrees. Line muffin tin with paper liners and grease with coconut oil or your choice of oil.
  2. Whisk together the flax and water; allow to thicken. This replaces the egg in the recipe.
  3. Whisk together the dry ingredients: flour, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger.
  4. Melt the coconut oil and then pour into a large mixing bowl with vanilla and the flax mixture. Stir in the sugar and pumpkin puree. Blend well.
  5. Gradually add the flour mixture and stir until just combined; avoid over-mixing. Gently fold in the chocolate chips.
  6. Scoop batter into muffin cups evenly and bake for 20 minutes or until a toothpick inserted comes out clean.
process of shots of how to make pumpkin muffins

Are Pumpkin Muffins Healthy?

I am obsessed with all things chocolate and pumpkin but it’s been a long time since I have had a healthy muffin that really tasted this fantastic. I promise that this Healthy Pumpkin Muffin will make the perfect addition to any breakfast or snack and it will become one of your favorite muffin options. It is perfect for a simple breakfast served with yogurt and fresh fruit or as a snack throughout week. The fact that these are healthier than your typical store bought muffin makes me a little more obsessed with them but most importantly my kids all loved them.

pumpkin muffins on a white plate

Can you freeze Healthy Pumpkin Muffins?

These are not a muffin that you can only eat one of so it’s a good thing they are healthy! I was able to make 18 perfect sized muffins. We usually double the recipe because they freeze so well! They will last 2-3 days at room temp, and up to 2 months in the freezer. Not that they ever last that long in my house!

pumpkin muffins on a cooling rack

More Healthy Muffin Recipes:

Healthy Pumpkin Muffins

These Healthy Pumpkin Muffins are made with whole wheat flour, nutrient-packed pumpkin, are lower in sugar, and are loaded with delicious pumpkin spices.
4.34 from 18 votes
Print Pin Rate
Course: Breakfast
Cuisine: American
Keyword: Pumpkin Spice Morning Muffins
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 18 Muffins
Calories: 164kcal

Ingredients

Instructions

  • Preheat oven to 375 degrees. Line muffin tin with paper liners or grease muffin tin cups.
  • Whisk together the flax and water; allow to thicken.
  • In a large mixing bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, nutmeg, ginger. Set aside.
  • In another bowl, melt the coconut oil and then add the vanilla and the flax mixture together. Mix in the sugar and pumpkin puree. Blend well.
  • Gradually add the pumpkin mixture into the flour mixture and stir until just combined; avoid over-mixing. Gently fold in the chocolate chips.
  • Scoop batter into muffin cups evenly and bake for 20 minutes or until a toothpick inserted comes out clean.
  • Allow to cool for 5-10 minutes on a cooling rack. Leftover muffins can be stored in the fridge for a few days or in the freezer for a month.
Tried this recipe?Mention @SuperHealthyKids or tag #SuperHealthyKids!

Nutrition

Calories: 164kcal | Carbohydrates: 22g | Protein: 2g | Fat: 8g | Saturated Fat: 6g | Polyunsaturated Fat: 0.4g | Monounsaturated Fat: 0.5g | Trans Fat: 0.01g | Cholesterol: 1mg | Sodium: 156mg | Potassium: 49mg | Fiber: 1g | Sugar: 11g | Vitamin A: 2135IU | Vitamin C: 1mg | Calcium: 31mg | Iron: 1mg

Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

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Recipe Rating




20 Comments

These muffins are so delicious!!! The coconut oil makes them melt in your mouth 🙂

I’ve made them with white flour, white sugar and allspice. One time I didn’t have chocolate chips and they were still super tasty.

Thank you for this yummy and healthy recipe.

I cannot get these muffins to turn out right for the life of me! The batter seems to be thicker than pictured when I make it, and the muffins don’t smooth out – they remain the same shape as when I dropped them in the muffin cups. The batter seems to be missing liquid, but like I’ve said, we have tried making them twice and run into the same issue both times so I don’t think it’s a mistake on our following the recipe. Is anyone else having this trouble? Is it a thicker batter than typical for muffins? On the bright side, my kids still love the taste. 🙂

Something that is different in this recipe is the fact that we are using flax as eggs. So this is a great recipe for those with an egg allergy. You could, if you prefer, use 2 eggs in place of the flax and water. Maybe it will offer you a better texture Brooke. 🙂

I had the same problem with the batter being really thick and they didn’t change shape in the oven. Taste good and could use as a crumble in yogurt, but not muffins. Does the flour used make a difference? I used a gluten free flour that subs for all purpose 1:1.

5 stars
BEST. MUFFINS. EVER. When we take them to friends, they rave about them and beg for the recipe. My diabetic friends literally cry when they learn it is gluten free. If this recipe is your sole contribution to the world, you have made it to heaven!