This healthy pumpkin muffin recipe is a delicious, low sugar fall breakfast. Naturally gluten + dairy free – these muffins are easy to make and so tasty!
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These healthy pumpkin muffins might be the best muffins we’ve ever made. And we have made a lot of muffins over the years!
Why we love these Gluten Free Pumpkin Muffins
There’s a lot to love about these pumpkin muffins. They’re delicious, easy to make, and a healthy alternative!
- low sugar & low fat– typically muffins are loaded with sugar and fat. These muffins only have 2g of fat per muffin and 13g of sugar. 13g of sugar might seem high – but most muffins have over 30g! The sugar in this recipe comes from all natural honey.
- whole grains – I made these pumpkin muffins with oat flour.
- simple ingredients– there are no weird flours or funky ingredients here! Just simple ingredients you have in your fridge/pantry – waiting to be used up in these delicious muffins!
- flavor from spices– Most of the flavor in these healthy muffins comes from pumpkin spice, rather than fat or sugar.
I’ll admit it, I’m one of those people that LOVES pumpkin, so it was easy to fall in love with these muffins.
Ingredients
To make these healthy pumpkin muffins, you’ll only need a few basic ingredients.
- oat flour
- pumpkin puree
- honey
- baking soda
- almond milk
- eggs
- pumpkin pie spices: cinnamon, nutmeg, ground ginger, ground cloves
- Mini chocolate chips are optional, but encouraged!
Substitutions
There are A LOT of ways to customize these healthy pumpkin muffins to your taste buds/dietary needs. Here are a few:
Milk: You can use any milk you like in this recipe. Dairy or non dairy (almond, soy, oat, coconut) will all work
Oat Flour: You can make your own oat flour following this oat flour recipe. You can’t use coconut flour or almond flour in this recipe. I haven’t tried this recipe with whole wheat flour but I think it would work!
Sweetener: You can sub maple syrup for the honey in this recipe.
Add ins: I like adding chocolate chips. Chopped nuts, dried cranberries, or seeds are also delicious
Warm Spices: You can use 3.5 teaspoons of pumpkin pie spice in these muffins. If you do not have nutmeg or cloves, just add a little bit more cinnamon/ginger.
Pumpkin: If you’re out of pumpkin, you can use mashed bananas. You could also make these Healthy Banana Muffins!
Sweet Potato: Try this Sweet Potato Muffin Recipe!
Vegan: I have not tried making these muffins vegan, but you might be able to substitute the eggs with flax eggs. You can substitute maple syrup for honey.
High Protein: We love these Pumpkin Protein Muffins as a higher protein fall muffin (9g per serving).
Bread: I haven’t tried making this recipe into a pumpkin bread, but you can try our healthy pumpkin bread recipe!
I love this non stick muffin tin or these silicone muffin liners for baking muffins.
You can find substitutions for all of these ingredients in the green shaded box below.
Is pumpkin puree the same as canned pumpkin?
Yes! Pumpkin puree and canned pumpkin are the same things. Make sure you are buying pumpkin puree or canned pumpkin and not pumpkin pie filling. Pumpkin Pie filling has sugar and spices added.
If you love pumpkin, you have to checkout these 34+ Healthy Pumpkin Recipes!
How to make Healthy Pumpkin Muffins
Making healthy pumpkin muffins is super easy.
- In a large bowl or stand mixer, combine maple syrup, pumpkin puree, eggs, and milk.
- Once combined, add in baking soda, cinnamon, nutmeg, ground ginger and cloves.
- Add the oat flour to the wet ingredients. Mix until just combined (don’t over mix!)
- Gently fold in chocolate chips. Pour batter into greased or lined muffin tins. Sprinkle with extra chocolate chips on top if you’d like.
- Bake at 350 for 20-25 minutes, until a toothpick comes out clean when inserted in the center of the muffins.
- Enjoy with a vanilla latte!
Storage Options
These low fat pumpkin muffins won’t last long in your house. I love to snack on them with a Low Sugar Pumpkin Spice Latte!
Storing: Let the muffins cool at room temperature, then store these muffin in the fridge for up to a week to maintain freshness. You can leave them out of the fridge, but they will not last as long because they’re very moist and will get moldy.
Can you freeze pumpkin muffins?
Yes you can freeze these pumpkin muffins! Allow the muffins to cool, then store them in an airtight container or ziploc bag in the freezer. To defrost, leave out the night before in the fridge and they will thaw out. Or, just pop in the microwave for 1-2 minutes directly from the freezer
FAQs
Yes, you can use 3.5 teaspoons of pumpkin pie spice in these muffins instead of individually measured spices.
Adding pumpkin to your baked goods moist and dense. It doesn’t have too much of a taste but when combined with cinnamon and ginger it gives a delicious fall flavor to meals.
No, you can eat canned pumpkin raw. It’s completely safe to eat!
Pumpkin muffins are dense due to the canned pumpkin and eggs. They make muffins thick and rich!
Other healthy muffin recipes you’ll love:
We love healthy muffin recipes so much that we created a whole free muffin ebook about them! You can get it here or check out these 30+ Healthy Muffins:
Healthy Pumpkin Muffins
Ingredients
- 1/2 cup maple syrup or honey
- 1 1/2 cups pumpkin puree
- 2 eggs
- 1/4 cup milk regular or nondairy
- 2 teaspoons baking soda
- 2 teaspoons cinnamon
- 1/2 teaspoon nutmeg
- 1/2 teaspoon ground ginger
- 1/2 teaspoon cloves
- 2 cups oat flour gluten free if necessary
- 1/2 cup chocolate chips
Instructions
- Preheat oven to 350 + prepare a greased or lined muffin tin.
- In a large bowl or stand mixer, combine maple syrup, pumpkin puree, eggs, and milk.
- Once combined, add in baking soda, cinnamon, nutmeg, ground ginger and cloves.
- Add the oat flour to the wet ingredients. Mix until just combined (don't over mix!)
- Gently fold in chocolate chips.
- Pour batter into greased or lined muffin tins, filling each cup with about 1/3 cup batter. Sprinkle with extra chocolate chips on top if you'd like.
- Bake at 350 for 20-25 minutes, until a toothpick comes out clean when inserted in the center of the muffins
Video
Notes
- Milk: You can use any milk you like in this recipe. Dairy or non dairy (almond, soy, oat) will all work
- Sweetener: You can sub maple syrup for the honey in this recipe.
- Add ins: I like adding chocolate chips. Nuts, dried cranberries, or seeds are also delicious
- Spices: You can use 3.5 teaspoons of pumpkin pie spice in these muffins. If you do not have nutmeg or cloves, just add a little bit more cinnamon/ginger.
- Vegan: I have not tried making these muffins vegan, but you might be able to substitute the eggs with flax eggs. You can substitute maple syrup for honey.
Kathy M says
Why so much baking soda? They had so much that they tasted like it when they were baked… I was also wondering why you didnt use any baking powder in them?
The Clean Eating Couple says
I haven’t had someone say this tastes like baking soda and these have many reviews – so I’m sorry you felt that way! That’s what I chose for the leavening agent in this recipe. I haven’t tried it with baking powder.
Esther Esau says
My go to pumpkin muffin! Made these over five times in the fall time . They turn out great everytime ! You’d never tell it wasn’t made without white flour .
Rachelle says
You mentioned sweet potatoes in the substitutions. Do you think it would work to swap with the pumpkin? Thanks
The Clean Eating Couple says
I haven’t tried that, but if you want a sweet potato muffin recipe, you can just make this Sweet Potato Muffin!
BSD says
I haven’t made this recipe yet, but plan to make it soon. But, can you clarify something in the notes/substitutions which on one hand says:
Oats: You can sub old fashioned rolled oats for 2 cups of oat flour.
And on the other hand says:
Blender: If you don’t have a blender, you can make these in a mixing bowl. I’d recommend using oat flour. You can’t use whole oats to make this recipe, they will not cook.
Would you clarify? Thank you.
The Clean Eating Couple says
i’m not sure what part you need clarification by – I’m sorry! You can’t use whole oats in this recipe – you need to use oat flour. I was just saying if you don’t have a blender, you can use a mixer to mix the muffin batter, not to mix oats.
Chris Fobbe says
This recipe was so simple and so delicious. My daughter has to eat GF and she said they are amazing! I thought they were amazing too and I am not a fan of GF baked items. Both the taste and texture are excellent!
Taylor says
So easy to make and super delicious! My 2 year old loves them too!
Cate says
Wonderful as muffins. We had extra batter and tried as pancake…yum! Could also make a 9×9 cake. Very versatile.
Meg says
Is applesauce a possible substitute for the honey or maple syrup! I plan to make them this weekend and I’d like to reduce the honey (and do not like maple syrup) and have seen other healthy- type recipes use unsweetened applesauce. Looking forward to trying them!
The Clean Eating Couple says
No, applesauce would completely change the batter and make it too wet. You can try reducing the honey a little bit but definitely don’t try applesauce!
debbie says
hello. is there a way to turn this recipe into cookies? thank you
The Clean Eating Couple says
Unfortunately no but you can try these!
Celeste says
This was a great recipe to try! Thank you for creating and sharing it! I didn’t measure the chocolate chips that I used and the muffin I did try (with more to sample soon) was wonderful! Keep up the great work!
Lucy Garcia-Storey says
I’d give it a six if I could. My daughter turned me onto these muffins, and they are dangerously delicious. I love the texture and the fact that they’re not yucky sweet. We topped it with Enjoy Life regular and chunky Chocolate Chips which are fantastic. The only problem I can fine with this recipe is the fact that you can’t eat just one. I find myself grazing.
Cristina Mitchell says
Can you add cocoa powder instead of chocolate chips to make them swirl chocolate pumpkin?
The Clean Eating Couple says
I don’t think that would taste very good! Cocoa powder is pretty bitter so it might need something sweet to counteract it. You could skip the chocolate chips if you don’t want them.
Carolina De Zan says
Thank you for this delicious recipe! Just tried it out because I had canned pumpkin I wanted to use up. They turned out so good! I like that they’re just the right amount of sweetness and that was without the added chocolate chips on top. This recipe is too good to only be used in the fall! I made them for my 13 yr old son to take to school as a snack and I’m sure he’s going to love them!
Krista says
Truly THE BEST healthy pumpkin muffin out there!! I used a little less maple syrup but replaced the sugar by adding more chocolate chips on top of muffin 🙂 They came out absolutely perfect!!
Madelyn says
These are so good and so moist!!!! I made my own oat flour with a food processor (which is so easy and less expensive than buying a bag of it!), and used pumpkin spice and a little extra cinnamon and ginger instead of the individual spices and they came out perfect. I’ve been heating them up for breakfast and putting cream cheese on them.
Melinda says
These are so good! Quick and easy to make. I will definitely be making these again!
Riley says
I love these muffins, they turned out great! I added one teaspoon of vanilla extract and two pinches of salt to the batter.
Carina says
These are incredible!!! Such great flavor and full of healthy ingredients! you can’t beat this!
Barbara says
These have become a mid-morning snack staple in our house. I have added raisins to the muffins which we like a lot. Thanks for the very delicious and relatively healthy addition to our menu.
Lauren says
Have you ever made them in the ninja foodie? How would you adjust the time?
The Clean Eating Couple says
Sorry but I have no idea! I don’t have a ninja foodie
K says
I was wondering if I could reduce the amount of maple syrup or would they get to dry and not sweet enough?
The Clean Eating Couple says
Probably wouldn’t recommend it because I think they would be dry and not as sweet
Sam says
They came out great and were easy to make! I will be making these for when I go to work.
Paula says
So delicious! Finally made some this morning because I’d been craving them for about 2 weeks!
Barbara says
We love these amazingly moist and delicious muffins. We add raisins instead of chocolate chips and they’re perfect.
Cindy says
Hi, I just made these last night & they were soo delicious!! This recipe will be my go to from now on. Thank you for sharing 👍