Perfect Pumpkin Chocolate Chip Muffins (Easy low sugar muffin recipe!)

These easy and healthy pumpkin chocolate chip muffins are light, sweet, and are ready in less than 30 minutes. Plus they contain no sugar or refined flour and are the perfect Fall snack, breakfast, or dessert. 

Pumpkin Chocolate Chip Muffins | The easy and healthy pumpkin chocolate chip muffins are refined sugar free! | A Sweet Pea Chef

I’ll be the first to tell you I am no baker. In fact, baking powder, baking soda, yeast, breads, and cakes kinda freak me out. All of them, yes.  I’m much more comfortable with quick breads (like this bread or these muffins) and, quite honestly, foods completely unrelated to baking.

Nonetheless, I do enjoy EATING baked foods. Particularly during Fall when pumpkin muffins and other baked pumpkin treats are everywhere.

And well, I am a food blogger. So, technically, this is kinda my job.

Ever since I made my Healthy Banana Chocolate Chip Muffins and they turned out so well, I’ve had my eye on more muffin recipes.

And, given it’s pumpkin season, I have to be able to test as many pumpkin recipes as possible. Healthy pumpkin recipes. So, as you can imagine, these pumpkin chocolate chip muffins HAD to happen.

These pumpkin muffins are not your typical pumpkin muffins, they are – DRUMROLL – healthy pumpkin muffins. The chocolate chip pumpkin muffins are not only an amazing dessert or snack, but they are also healthy pumpkin breakfast muffins you can enjoy every morning guilt-free.

This healthy pumpkin muffin recipe doesn’t require refined sugar or flour. But the pumpkin chocolate chip muffins are so moist, sweet, and delicious. I’m sure you’ll fall in love with them.

Because pumpkin and chocolate needs to happen in our lives.

Bowl of dark chocolate chips that will be used in the pumpkin chocolate chip muffins.

How To Make Muffins Healthy

Not all pumpkin muffins are created equal, especially if you’re talking about store-bought pumpkin muffins or pumpkin chocolate chip muffins, which often contain high amounts of sugar, refined flours, and partially hydrogenated fats — not good.  The benefit of making your own homemade muffins is you can completely control what goes in them.

Here’s how I make any muffin recipe healthy, including these pumpkin chocolate chip muffins.

  • Replace all-purpose flour with an unrefined flour, such as spelled flour, buckwheat flour, or whole wheat pastry flour. This adds nutrients and removes empty, non-beneficial, and processed carbs.
  • Replace any butter or oils with melted coconut oil or mashed fruit, like banana, applesauce, or pumpkin puree.
  • Replace milk chocolate chips with dark chocolate chips. Choosing chocolate with a high cacao percentage, at or above 70%, means there is minimal sugar in the chocolate.
  • Replace any sugar with either mashed fruit or a healthier, less refined sweetener, like pure maple syrup, coconut sugar, or raw honey. Read more on quitting sugar here.

Follow these easy tips and you’ll be on your way to healthy, delicious muffins in no time!

Mixing bowl filled with the muffin batter, which includes pumpkin puree, mashed banana, spelt flour, egg, pure vanilla extract, cinnamon, and is topped with the dark chocolate chips that will be folded in before baking.

How To Make Muffins Without Sugar

Replacing the sugar in this pumpkin chocolate chip muffin recipe is shockingly easy. Keep in mind that fruits contain natural sugars so these muffins fall under the category of low sugar pumpkin muffins and definitely free of refined sugar.  The trick is to use natural sweeteners that have actual nutritional value and avoid the heck out of white and brown sugar and high fructose corn syrup.

Here are 3 ways to naturally sweeten your muffins:

  1. Mashed Fruit: Use mashed fruit, like mashed banana, pumpkin puree, or unsweetened applesauce. The natural sweetness of those fruits makes up for not adding in any extra sugar. And adding banana to pumpkin muffins means you get to enjoy delicious pumpkin banana muffins. You get the best of 2 worlds and ZERO added sugar involved. Happy life. Am I right?
  2. Spices: Add in additional cinnamon and pure vanilla extract, both of which make the food taste even sweeter. Plus, adding extra cinnamon to pumpkin muffins is always a good idea.
  3. Natural Sweeteners: Add raw honey, pure maple syrup or coconut sugar if you want your pumpkin muffins to be extra sweet while maintaining their refined sugar free healthy pumpkin muffins status at the same time.  Though, this recipe really does’t really need any added sweeteners.

Muffin tin filled 3/4 way full with the pumpkin chocolate chip muffin batter and then topped off with additional dark chocolate chips before being placed in the oven.

How To Substitute Spelt Flour

Instead of spelt flour, you could also use the following as an easy substitution:


  • whole wheat pastry flour
  • cassava flour (GF, nut-free)
  • almond flour (GF)


  • coconut flour – but you’ll need to add more liquids


  • oat flour – you’d need to add in a little more oat flour than what’s called for with the spelt flour

Spelt flour has recently become very popular because it is a good alternative for wheat for people who cannot tolerate wheat. Spelt does contain gluten, however, so people with gluten allergies or celiac disease do need to avoid it.

Close up of a side shot of the pumpkin chocolate chip muffins on a cooling rack, ext to several other muffins and dark chocolate chips.

How To Make Pumpkin Chocolate Chip Muffins Without Eggs (Vegan)

This healthy pumpkin muffin recipe uses one egg, which is the only non-vegan ingredient. Fortunately, it’s easy to replace the egg if you’d like to make these vegan muffins using a flax egg. Flax “eggs” are an easy vegan egg substitute. They’re a great baking alternative for eating vegan and for those who have allergies to eggs.  To do so, you’ll need to make one flax egg, which is made by combining flaxseed meal and water.

To make 1 flax egg, combine:

  • 1 tablespoon of ground flaxseed
  • 3 tablespoons of water

Stir well, and then allow the mixture to set for about 5-10 minutes.  Then, use as you would a regular egg.  This can also be done using ground chia seeds.

There you have it – vegan pumpkin chocolate chip muffins with a simple egg substitute!

You could also add additional pumpkin puree and mashed banana, if you’d prefer.

Close up of the baked pumpkin chocolate chip muffins, removed from the oven and ready to set out on a cooling rack.

How To Freeze Muffins

Yes, you can easily freeze these pumpkin muffins.  If you’re able to not eat all of these muffins in one sitting or have a bunch of sweet kiddos with puppy dog eyes, you can easily freeze muffins to save for later.  Follow these easy steps to freeze:

  1. After baking the muffins, let them cool completely.
  2. Place the pumpkin muffins on a baking sheet lined with parchment paper.
  3. Place the baking sheet in the freezer for about 1-2 hours.
  4. Once the muffins are completely frozen, place them into freezer-safe bags or containers to keep until ready.

Frozen muffins will last in the freezer for up to 3 months.  When ready to enjoy, allow to thaw in the refrigerator or on the counter.

Pumpkin chocolate chip muffins that have been baked and are now cooling on a cooling rack, ready to eat.

More Healthy Pumpkin Recipes

Since pumpkin is in season, you’re probably in need of more pumpkin recipes, am I right?  And, since I love pumpkin so dang much, I, of course, have got what you need!

So much pumpkin goodness!!

Healthy Pumpkin Recipes For Fall

5 from 6 votes
Pumpkin Chocolate Chip Muffins Square Recipe Preview Image
Pumpkin Chocolate Chip Muffins
Prep Time
8 mins
Cook Time
20 mins
Total Time
28 mins

The easy and healthy pumpkin chocolate chip muffins are light, sweet, and are ready in less than 30 minutes. Plus they contain no sugar or refined flour!

Categories: Baking, Bread, Breakfast
Difficulty: Easy
Keyword: healthy pumpkin chocolate chip muffins, pumpkin chocolate chip muffins, pumpkin puree
Servings: 12 muffins
Calories: 163 kcal
Author: Lacey Baier
  • 1 egg*
  • 3/4 cup pumpkin puree
  • 1 cup unsweetened almond milk
  • 1 tbsp freshly squeezed lemon juice
  • 1/4 cup mashed ripe banana (about 1 medium banana)
  • 2 tbsp coconut oil, melted
  • 1 tsp pure vanilla extract
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 tsp sea salt
  • 1 tsp ground cinnamon
  • 1/4 tsp ground nutmeg
  • 1 1/2 cups spelt flour
  • 3/4 cup semisweet chocolate chips, plus more for topping
  1. Preheat oven to 375 degrees F and grease a muffin tin with coconut oil.

  2. In a small mixing bowl, combine the almond milk and lemon juice and let sit for 5 minutes.  This will create the "buttermilk."

  3. Add pumpkin puree, almond-lemon buttermilk, egg, mashed banana, oil, and vanilla extract to a large mixing bowl, and stir together to mix well.

  4. In a separate mixing bowl, combine the spelt flour, sea salt, baking soda, baking powder, nutmeg, and cinnamon.

  5. Combine dry and wet ingredients and stir together.

  6. Add the dark chocolate chips and fold in, stirring until just incorporated.

  7. Spoon the batter into the muffin cups until each cup is filled almost all the way full.

  8. Sprinkle a few more dark chocolate chips on top, if desired.

  9. Place in the oven and bake for 18-20 minutes or until golden brown on top and a toothpick inserted into the center comes out clean.

  10. Transfer to a cooling rack to cool completely.

Recipe Video

Recipe Notes

* To replace the egg with 1 flax egg, combine 1 tablespoon ground flaxseed with 3 tablespoons water.  Stir well, and then allow the mixture to set for about 5-10 minutes.  Then, use as you would a regular egg.  This can also be done using ground chia seeds.

Nutrition Facts
Pumpkin Chocolate Chip Muffins
Amount Per Serving (1 muffin)
Calories 163 Calories from Fat 60
% Daily Value*
Fat 6.7g10%
Saturated Fat 3.4g17%
Cholesterol 13.3mg4%
Sodium 123.2mg5%
Carbohydrates 25g8%
Fiber 5.8g23%
Sugar 8.5g9%
Protein 5.8g12%
* Percent Daily Values are based on a 2000 calorie diet.

This post contains affiliate links for products I use regularly and highly recommend.

Lacey Baier

Hey there! I’m Lacey Baier and I’d like to welcome you! I’m a healthy lifestyle influencer and the creator of this clean-eating blog and YouTube channel, as well as cleanish, my clean-eating supplement brand. My recipes have been published on Food Network, Good Morning America, FoxNews, Tastemade, Fitness Magazine, and much more. I live in Austin, Texas with my husband and four kiddos. Let’s get started!

15 thoughts on “Perfect Pumpkin Chocolate Chip Muffins (Easy low sugar muffin recipe!)

  1. 5 stars
    I made these muffins and they turned out amazing! The whole family loved them. Thank you! I saw the suggestion for freezing them but if we want to munch on them for a few days do you recommend storing at room temp. Or in the refrigerator?

    1. Hi Leah, thank you so much for commenting! We’re really happy that you like these muffins (it’s a crowd favorite!). I’m Lacey’s blog moderator and can help you with your question. After discussing with her, here’s the deal on muffin storage…the refrigerator is generally NOT the way to go because the cool temperature will dry them out. Best way is to place them in an airtight container – or zip-lock bag – with a paper towel on the bottom and over top of the muffins. Room temperature. The airtight container will help to keep them moist, while the paper towel will help keep them from going soggy. For best results, store them in a single layer…hope this helps! -Jen

  2. Hi, what other floor would you recommend besides spelt? I have almond flour and can also grind up some old
    Fashioned rolled oats into an oat flour.

  3. I made these last week, the temperature for baking was 450 for the first 5 minutes then reduce to 350 for 15 to get a nice round top.

  4. It’s the texture of the dou is the texture of the dough supposed to be crumbly? I feel like I messed up somewhere. I did use coconut flour-I kind of feel like I read somewhere I should be adding more liquid. The flavor was there but the texture was awful. I think I’m going to crumble then up and add more liquid or egg whites something to bind them and bake them again.

  5. Is it possible to use almond flour ? In the recipe ( for the banana chocolate chips muffins as well) as a replacement for spelt flour.

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