Hi friends! Boy do I have a delicious baking project for you to try ASAP – this Healthy Pumpkin Chocolate Chip Muffins recipe. I’ve had this recipe on repeat this fall season. Hungry for more? Let’s jump in!

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Whole Grains and No Refined Sugar

Here’s the finished product. Moist, made with whole grains, sweet but not too sweet, and made without refined sugar. What’s not to like?

Great Use of Leftover Ingredients

This recipe is a great use for leftover canned pumpkin (at least 1 cup), chocolate chips (since you only need a 1/2 cup), and/or pumpkin pie spice (you’ll need 1 1/2 teaspoons).

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

And you could use regular flour, but spelt is great in this recipe and makes it whole grain.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Muffin Recipe with Almond Milk

While dairy milk would likely work just fine, I used almond milk to make this batch of my Healthy Pumpkin Chocolate Chip Muffins recipe.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

I used Tollhouse chocolate chips, but you’d need to make sure you use a vegan option to keep the recipe 100% vegan. And likewise that the ingredient list doesn’t contain refined sugars to keep it refined sugar free. You can find great options at a health food store, like Whole Foods.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Have you guys tried these parchment-paper-like muffin cups? I love them!

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Two Versions of This Healthy Pumpkin Chocolate Chip Muffins Recipe

There are two versions of this Healthy Pumpkin Chocolate Chip Muffins recipe. One is made with more pumpkin and the other more almond milk. The above photo features the batter with more pumpkin. And as you can see, it’s quite thick. If you check the notes in the this Healthy Pumpkin Chocolate Chip Muffins recipe, you’ll see there’s an option to make this with more almond milk instead of more pumpkin. The latter will yield a slightly more liquidy batter.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

In fact all of the photos in this recipe are from the more-pumpkin version of this Healthy Pumpkin Chocolate Chip Muffins recipe.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Because the batter is thicker, it doesn’t rise as much.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

How to Get Extra-Tender and Moist Muffins

But the extra pumpkin makes this version of the recipe extra moist and tender. I think I like it better, though I wanted to provide another option in case you only had one cup of canned pumpkin.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Don’t you just want to dig in? Yum!

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Homemade Muffins > Store-Bought Muffins

This clean eating recipe is super easy and yields delicious results. It may be my favorite creation for the whole year! When I eat something like this that is so tasty while being pretty darn good for you too, it makes it hard to eat store bought / coffee shop muffins. I mean, most of those are made with white flour and other processed ingredients. Not to mention waaaay too much sugar. Yup, I’ll take these!

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

These are perfect to go along with the rest of your breakfast. And as you can see, I enjoyed it with a fried egg and some fresh fruit.

You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

And it’s really cute stored in mason jars, especially if you’re planning to gift a couple to a friend or loved one.

Print
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You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Healthy Pumpkin Chocolate Chip Muffins Recipe | Whole Grain, No Refined Sugar, Vegan

  • Author: Diana of thechiclife.com
  • Prep Time: 10 mins
  • Cook Time: 20 mins
  • Total Time: 30 mins
  • Yield: 12 1x

Description

This Healthy Pumpkin Chocolate Chip Muffins Recipe is so delicious, you won’t believe it’s healthy. Made with whole grains, it’s also refined sugar free and vegan.


Ingredients

Scale
  • 2 cups spelt flour (or sub flour of choice)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1 1/2 teaspoons pumpkin pie spice (or sub cinnamon)
  • ¼ teaspoon salt
  • ½ cup chocolate chips (use vegan / no refined sugar to stay in line with the theme of this recipe)
  • 1 flaxseed egg (1 tablespoon ground flaxseed mixed with 3 tablespoons water – let sit for about 10 minutes) (or sub an egg if you want to make it non-vegan)
  • ½ cup coconut palm sugar (or sub sugar of choice)
  • 1 ½ cups canned pumpkin
  • 1/2 cup almond milk (or sub milk of choice)
  • 3 tablespoons canola oil (or other oil of choice)
  • 1 teaspoon vanilla extract

Instructions

  1. Pre-heat oven to 350 degrees F and prepare a 12 cup muffin tin with non-stick spray or muffin liners.
  2. In a large bowl, prepare the flaxseed egg.
  3. Add spelt flour, baking powder, baking soda, and pumpkin pie spice into a medium bowl and whisk together. Add chocolate chips and whisk in.
  4. In the wet ingredient bowl, add coconut sugar and whisk to the flaxseed egg till combined.
  5. Whisk in pumpkin, almond milk, canola oil, and vanilla extract.
  6. Pour dry ingredient mixture into the wet ingredient mixture, and stir gently just to combine – careful to not over-mix.
  7. Pour/spoon muffin batter into muffin cups – about ¾ full each. Use spatula to flatten tops if needed. This batter is SUPER thick, guys.
  8. Bake for 18-22 minutes until centers set or a toothpick inserted in the center of a muffin comes out clean.
  9. Cool at least 10-15 minutes, or until safe to eat, before serving. Enjoy!

Notes

Pumpkin makes this batter really-really dense. It may take some extra time to bake and you may notice a toothpick inserted into the middle comes out sticky for a bit. This is expected but once it comes out clean, you’ll have a super moist and tender muffin. For comparison, I baked mine for 21 minutes total (16 + 3 + 2 with two toothpick checks). It may take a little less time for you if you don’t open the oven door twice like I did.

If you prefer to use or only have 1 cup of pumpkin, you can use that but you must also increase the total almond milk used to 3/4 cup total (which is 1/2 more than the original recipe used).

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Keep That Muffin Party Going

Best of all, after making a batch, I freeze what I don’t eat immediately so I can have fresh muffins at my heart’s desire. I simply pull one out, let it thaw for at least 30 minutes and then bake it at 350 degrees F for about 5-6 minutes. The re-baked muffins taste almost just like fresh baked muffins all over again?

More Delicious Clean Eating Recipes

Healthier Baked Pumpkin Doughnuts Recipe

Chocolate Chip Muffins Recipe Made with Almond Milk

Healthy and Clean Eating Turkey Tetrazzini Recipe

Healthy Pumpkin Pie Oatmeal Recipe

Autumn Granola Recipe (Oil-Free, Made with Canned Pumpkin)

Healthy Chai Tea Latte Recipe

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Thanks for reading! Hope you enjoy this whole grain and refined-sugar-free Healthy Pumpkin Chocolate Chip Muffins Recipe. Cheers!

Oh, and I made a shareable graphic in case you’d like to spread the love of healthy sweets to your friends and loved ones:

You won't believe these delicious muffins are healthy! Yes, a Healthy Pumpkin Chocolate Chip Muffins recipe. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

I can't stop making these healthy pumpkin chocolate chip muffins! They're delicious, clean eating, and vegan. Loving them for breakfast AND dessert! #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe