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The Best Healthy Pumpkin Muffins (Gluten Free + Vegan)


These healthy pumpkin muffins are about to become your new go-to recipe for weekend baking activities this fall. They are moist, flavorful, and full of healthy ingredient swaps. Not to mention, they are refined-sugar free, gluten free and vegan friendly. 

There’s a reason they are called, “The Best Healthy Pumpkin Muffin,” and now it’s your turn to make them and see why! 

Starbucks seems to set the tone for upcoming holidays. When the pumpkin spice latte debuts on the menu, it’s as if we can all take a deep breath and inhale crisp, fall air knowing that the holiday season is upon us. 


The pumpkin spice latte might be the mascot of Fall, but pumpkin muffins and bread are a close second. 

The interesting thing about pumpkin muffins and bread is that the flavor we all know and love is actually trademarked by the spices, not the actual pumpkin. Although you wouldn’t want to leave the pumpkin puree out, because it provides a natural orange hue and moistness to the batter. 

These Healthy Pumpkin Muffins are a great alternative to Starbucks’ Pumpkin Bread

Starbucks might be known for their PSL, but it’s kind of a no brainer to grab a slice of their pumpkin bread while you’re at it. It seals the deal if you’re looking for the ultimate fall flavor experience. 

Even though the holidays are full of sweets and treats, the excess sugar can quickly wear us down. It’s a balance between embracing indulgence and mindfulness around what, when, and how often. 


If you love the flavors of fall, but are looking for alternatives that will help you feel your best, then I’ve got just the recipe for you. 

These healthy gluten free and vegan pumpkin muffins are everything your heart desires and more. The pumpkin muffins are moist, full of flavor, and include healthy baking swaps that allow for an indulgence that can be made more often. 

Related Post: No Bake Pumpkin Pie Cheesecake Bars

With so many pumpkin muffin recipes out there, why choose this one? 

I’m going to let you in a little secret. I’ve found a genius egg replacement to make recipes vegan friendly. Can you guess what it is? 


You heard that right. The brine from a can of garbanzo beans


When eggs are used in baking, it allows for a nice rise to the muffin tops and a moist, cakey interior. In order to get the same effect, aquafaba most closely resembles the traits of an egg. It results in a light and fluffy muffin. 

As a guide, 3 tablespoons of aquafaba = 1 egg. 

I mentioned earlier how these healthy pumpkin muffins closely resemble the Starbucks pumpkin bread. Let’s do a comparison analysis to see how the nutrition data is improved upon as a result of using healthy baking swaps. 

Starbucks Pumpkin Bread

  • 1 slice 
  • 410 calories
  • 15g total fat
  • 2.5g saturated fat
  • 500mg sodium
  • 63g total carbohydrates
  • 2g dietary fiber
  • 39g sugars
  • 6g protein 

The Best Healthy Pumpkin Muffins

  • 1 muffin
  • 231 calories 
  • 14g total fat
  • 6g saturated fat (MCTs from coconut oil)
  • 142 mg sodium
  • 22g total carbohydrates
  • 3g dietary fiber
  • 10g sugars 
  • 5g protein 

Pretty significant nutritional improvement, right? 

Here are the healthy baking swaps made for the Healthy Pumpkin Muffins: 

  • A combination of oat flour and almond flour instead of all-purpose flour
  • Almond milk instead of cow’s milk for a dairy free alternative
  • Coconut sugar in place of brown sugar for a low-glycemic sweetener
  • Maple syrup instead of cane sugar 
  • Coconut oil instead of canola and/or soybean oil for a healthier source of plant-based fats
  • Aquafaba as an egg replacement to make these muffins vegan friendly 

The best part about these healthy pumpkin muffins is that they taste just as good as the Starbucks pumpkin bread. Maybe even better.

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The Best Healthy Pumpkin Muffins (Gluten Free + Vegan)

  • Author: FitLiving Eats by Carly Paige
  • Prep Time: 10 minutes
  • Cook Time: 25 minutes
  • Total Time: 35 minutes
  • Yield: 12 muffins 1x
  • Category: Breakfast
  • Method: Baked
  • Cuisine: American
  • Diet: Gluten Free


Move over Starbucks pumpkin bread. There’s a new pumpkin muffin in town, and it’s full of healthy baking swaps but just as tasty. These aren’t called, “The Best Healthy Pumpkin Muffins” for no reason, and now it’s your turn to find out why. I’ll even let you in on my sneaky vegan egg replacement. It’s not what you think!


Units Scale


  1. Preheat the oven to 350F. 
  2. In a large mixing bowl, add the dry ingredients (oat flour, almond flour, coconut sugar, pumpkin pie spice, cinnamon, baking powder, baking soda and salt). Mix to combine. Next, add the wet ingredients. Stir in the pumpkin puree, almond milk, maple syrup, aquafaba and vanilla extract, then add the coconut oil. This prevents that coconut oil from solidifying after coming in contact with chilled almond milk. Mix until well incorporated. 
  3. Lightly grease a muffin tin with cooking spray. Divide the batter evenly among the 12 cups using a ⅓ cup measuring cup. Garnish with rolled oats or pumpkin seeds, if desired. 
  4. Bake for 25 minutes, until golden brown and fluffy. The muffin should spring back when lightly touched. Remove from the oven and allow to cool slightly before enjoying. 
  5. Store in the refrigerator for up to 1 week, or the freezer for several months. 


If you don’t have a can of garbanzo beans on hand, you could substitute aquafaba for 1 flax egg, or 1 whole egg. 


  • Serving Size: 1 muffin
  • Calories: 231
  • Sugar: 10g
  • Sodium: 142 mg
  • Fat: 14g
  • Saturated Fat: 6g (MCTs from coconut oil)
  • Carbohydrates: 22g
  • Fiber: 3g
  • Protein: 5g

Keywords: pumpkin, pumpkin bread, pumpkin muffins, healthy baking swap, gluten free pumpkin muffins, vegan pumpkin muffins, healthy pumpkin muffins, oat flour, almond flour, pumpkin puree, healthy baking

The Best Healthy Pumpkin Muffins 5

-Carly Paige

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Simply Swapped Everyday is your guide to elevating the everyday through mindful methods, ingredient swaps and over 75 plant-powered recipes. Cooking healthy foods at home has never been easier or more delicious!

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Hi! I’m Carly Paige, a culinary nutrition expert and chef who believes that healthy doesn’t have to be frustrating, boring or restrictive. I’m here to show you how through my Simply Swapped Method so that you can feel more energized and confident from within. You’ll find tips for focusing on nutrition in the kitchen, along with plant-powered, gluten-free recipes that proves healthy can be delicious.

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