Healthy pumpkin chocolate chip muffins are the perfect low-sugar breakfast or snack during the holidays! A welcome reprieve from sugar-laden holiday desserts, these low sugar healthy pumpkin muffins are sweetened with applesauce and maple syrup. They’re moist, flavorful, and filled with chocolate – what could be better?!

I’m a baker at heart. I love creating a good batch of cookies or muffins, making a gigantic mess, and savoring the end result.
The cleanup part? Not really my thing.
That’s why I married a man who also happens to enjoy doing the dishes. Thanks, Rich.
These healthy pumpkin chocolate chip muffins are my new favorite way to get the kitchen good and messy! It’s hands-down our favorite muffin recipe ever.
Even better, these muffins are guilt free and super low in sugar. Sorta like my delectable healthy pumpkin roll and pumpkin cream cheese bread.
They’re so good, in fact, that I’m planning to hoard as many cans of ALDI pure pumpkin as possible, so I can still make these after the holiday season is over.
Sorry, pumpkin pie lovers. You better get to ALDI real quick.

How to Make Healthy, Low-Sugar Pumpkin Muffins
The thing I like most about these muffins (aside from the fact that they’re melt-in-your-mouth moist and delicious), is that they are actually low in sugar.
Really!
These muffins are perfectly sweet and moist thanks to my secret weapon: applesauce.
Okay, it’s not so secret. But if I can have sweet muffins with less sugar that never get dry? I call it a win.
First, I made this recipe for classic pumpkin chocolate chip muffins from The Girl Who Ate Everything. They were divine. (Thank you, Christy!)
Then, I started thinking – how can I make these muffins healthier without sacrificing the deliciousness factor?
The original recipe calls for 2 cups of sugar. I decided to replace one cup of the sugar with one cup of applesauce. For the other cup, I used 1/2 cup maple syrup and 1/2 cup organic cane sugar. You could also easily use coconut sugar instead of cane. In fact, I probably will next time.
Then, I reduced the amount of oil (since there’s extra moisture in the sweetneners I used) and subbed coconut oil for canola.
The result? Sheer perfection.

Using Applesauce as a Sweetener in Healthy Pumpkin Muffins
Applesauce is a wonderful substitute for sugar in muffins or any baked recipe that yields a soft finished result. However, if you’re looking for a crispy texture (such as a sugar cookie), applesauce doesn’t work.
However, things like quick breads, cakes, and muffins are perfect candidates for using applesauce as a sweetener!
Also, keep in mind that when subbing applesauce, you should reduce the liquid in your recipe by 1/4. The substitution ratio is equal, as well – one cup sugar for one cup applesauce. And, be sure to choose an unsweetened applesauce at the grocery store – you’re trying to avoid sugar, remember?
Or, if you want to try your hand at applesauce-making, it couldn’t be easier! Here’s a simple recipe.
For more tips on using applesauce instead of sugar, read this post.
Another reason I love using applesauce in these healthy pumpkin chocolate chip muffins is that it enhances the fall flavor. Apples are a classic fall food that pairs perfectly with pumpkin and spices.
Ahhhhh, autumn vibes.
Other healthy baked goods you might like:
- Peanut Butter Chocolate Chip Muffins
- Gluten-Free Blender Pancakes
- Perfect Buttermilk Biscuits
- Soaked Blueberry Yogurt Pancakes
Healthy Pumpkin Chocolate Chip Muffins Recipe Notes

- You can try using an extra cup of applesauce to replace the maple syrup and sugar. However, you may want to reduce the coconut oil to 1/4 cup.
- You may also substitute 1 banana for the applesauce, or for the maple syrup/sugar.
- It’s best to slightly undercook these muffins for best results. Leaving them *slightly* gooey up-levels these from “good muffins” to “best muffins ever.” Don’t leave them too gooey obviously – you want to make sure the eggs cook thoroughly. Use the toothpick test to check doneness.
- I enjoy using Ghirardelli dark chocolate chips in this recipe. If you’re a purist, these Lily’s baking chips are sugar free and yummy.
- To simplify the baking process, I love using a large 2 dozen muffin tray so I don’t have to wash multiple trays. It’s the perfect size for this recipe.

Healthy Pumpkin Chocolate Chip Muffins
Healthy pumpkin chocolate chip muffins are the perfect breakfast or snack! These low sugar muffins sweetened with applesauce are a nice alternative to sugar-laden holiday treats.
Ingredients
- 4 eggs
- 1 can pure pumpkin puree, 15 oz.
- 1 cup applesauce, unsweetened
- 1/2 cup coconut oil, melted
- 1/2 cup maple syrup
- 1/2 cup organic sugar (or coconut sugar)
- 3 cups Wheat Montana non-GMO flour, or all purpose
- 2 tsp baking soda
- 1 tsp baking powder
- 1 TBSP pumpkin pie spice
- 1 tsp salt
- 2 cups dark or semisweet chocolate chips
Instructions
- Preheat oven to 400 F. Grease muffin pan or add paper muffin liners.
- Beat eggs, pumpkin, applesauce, maple syrup, sugar, and oil in a large bowl until smooth.
- Mix flour, baking soda, baking powder, salt, and pumpkin pie spice.
- Add flour mixture to pumpkin mixture and mix thoroughly, then fold in chocolate chips.
- Fill muffin cups almost full with muffin batter. Bake at 400 F for 15-17 minutes. Check them a minute or two early to check for doneness - don't overcook. Cool for several minutes before enjoying.
- Yield: 2 dozen muffins. These are even better the next day!
Notes
Adapted from The Girl Who Ate Everything original recipe.
Nutrition Information:
Yield:
24Serving Size:
1 muffinAmount Per Serving: Calories: 265Total Fat: 10gSaturated Fat: 7gTrans Fat: 0gUnsaturated Fat: 3gCholesterol: 31mgSodium: 238mgCarbohydrates: 41gFiber: 5gSugar: 18gProtein: 6g
Super easy to make. I love that they don’t dry out. I had to cook them longer but that’s just my oven. They are just the right amount of sweetness. Perfect breakfast treat for lazy summer days.
Yes, I love how they are moist too. Glad y’all enjoy them as much as we do! Thanks so much for the review!
These muffins sound great! Can I substitute the wheat flour for Almond flour?
You probably can, but it may change the texture
Would these work with spelt flour or all purpose gluten free flour? Two of us have to eat gluten free and two are fine with spelt flour.
Yes Christine, I think that will work just fine! Let me know how they turn out.
So delicious!!! Wow! I just pulled them out of the oven. Thank you!
So happy you love them! Thanks for leaving a review ❤️
Could this made as a bread instead of muffins? I dont have large muffin tins.
I think so! I’d say omit some of the eggs and just add one or two. If the batter is too runny, the bread loaf might not cook all the way through. I have a new pumpkin bread recipe releasing on the blog Monday!
I’m agnostic and not sure how I ended up on this site but this recipe is fairly simple and quick to make. So cheers to you Mary. Can’t wait to make them for the family I nanny for. ?
Cheers to you too Coleen! Glad you found out little corner of the internet!
What a refreshing cute. Keeps my sanity from the political lies and situation.
Thanks.
Thanks so much for visiting!
What a refreshing cite.
If I only have sweetened applesauce (homemade) should I just leave out sugar?
You could probably just reduce the sugar a little bit 🙂
Hi! I can’t wait to try these! Do you have any nutritional info?
I need to switch these to the new recipe card with the nutritional info. Thank you
Hello Mary. Cannot wait to try this recipe!!!! Can I substitute grated fresh pumpkin for the puree? I have an abundance of sweet pie pumpkins and would like to use them shredded. Thank you.
I bet you could! That sounds lovely. You may have to add some extra moisture, since the canned pumpkin is so moist.
These muffins are amazing! Thanks for the great recipe!
Thanks for the review!
Hi, just finished baking my first batch of these and they are so yummy! My hubby and I had them right out of the oven for breakfast with strong hot coffee. Nothing better on an early Fall morning!
They are deliciously moist and the flavor is delicate. My husband isn’t a big fan of pumpkin but he commented that he really enjoyed these muffins.
I’m watching my eating for health purposes so having the nutritional information would be most helpful.
Thank you for posting this recipe!
Thanks so much for the great review! Glad you enjoyed them!