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These Healthy Pumpkin Muffins are made with oat flour and are loaded with warming fall spices. They’re healthier than your average muffin while still being soft and fluffy and will be loved by the whole family!
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There’s nothing better than a batch of cozy pumpkin muffins baking in the oven on a crisp fall day. When I first shared these Healthy Pumpkin Muffins on the Choosing Chia Instagram, 2,000 people asked me for the recipe! They’ve quickly become a community favourite, and if you loved my viral Oat Flour Banana Muffins, you’re going to love these too.
These pumpkin muffins share a similar ingredient base with my Healthy Pumpkin Bread and Healthy Chocolate Pumpkin Bread, but the oat flour gives them a wholesome, fluffy texture that makes them feel extra nourishing. Oat flour is also a great gluten-free option; just make sure to use gluten-free certified oats. Enjoy them warm for breakfast, as a mid-day snack, or a healthy dessert.
When To Make These
- Fall baking days: These muffins capture all the best cozy fall flavours. Pumpkin spice, vanilla, and chocolate making them perfect for an easy recipe to bake on the weekends.
- Meal prep: Bake a batch on Sunday and enjoy them all week as an easy grab-and-go breakfast or snack.
- When you have leftover pumpkin purée: Use what’s left in the can after making Pumpkin Pie Overnight Oats or Pumpkin Spice Chia Pudding to make a batch of these muffins.
- Sweet moments: Make a batch to pair with a cup of tea or homemade chai latte to enjoy a sweet treat in the afternoon or after dinner.
Key Notes
*This is a recipe overview. The full recipe with measurements is below in the recipe card.
- Oat flour: you can use homemade oat flour which is made by blending oats, or buy oat flour from your local grocery store.
- Pumpkin puree: make sure to use pumpkin puree and not pumpkin pie filling. You can also make homemade pumpkin puree by roasting a pumpkin and blending it. Use any leftover puree to make a batch of Pumpkin Protein Balls or Healthy Pumpkin Banana Bread.
How To Make Healthy Pumpkin Muffins
Step 1: Add the eggs, avocado oil, maple syrup, pumpkin puree and vanilla extract in a bowl.
Step 2: Whisk together until combined.
Step 3: In a separate bowl, mix together the oat flour, baking powder, baking soda, salt and pumpkin pie spice.
Step 4: Mix the wet and dry ingredients together, then gently stir in the chocolate chips.
Step 5: Line a muffin pan with liners and spray with cooking spray to prevent sticking. Spoon the muffin batter into the moulds filling 3/4 of the way full.
Step 6: Bake at 350 degrees F for 18-22 minutes or until a toothpick comes out clean.
Recipe Variations
There are so many different variations you can bake from these healthy pumpkin muffins. Here are some ideas:
- Chocolate Pumpkin Muffins: Add 1/4 cup cocoa powder to the batter and use chocolate chips for a rich, double-chocolate version. If you love chocolate also try these Healthy Chocolate Zucchini Muffins.
- Pumpkin Mini Muffins: Scoop the batter into a mini muffin tin and bake for 10–12 minutes for bite-sized snacks.
- Pumpkin Bread Version: Pour the batter into a loaf pan and bake at 350°F for 45–50 minutes until golden and set.
How To Store
Store muffins in a sealed container at room temperature for up to 4 days or in the fridge for up to 7 days. If chilled, warm them in the microwave for a few seconds before eating.
To freeze, let the muffins cool completely, then transfer to a freezer-safe bag and freeze for up to 2 months. Thaw on the countertop and reheat in the oven or microwave before serving.
Jess’s Tips
- Use pure pumpkin purée: Make sure the label says 100% pumpkin, not pumpkin pie filling, which has added sugar and spices. Pumpkin purée is also great in this single serve Pumpkin Mug Cake.
- Mix gently: Overmixing makes muffins dense. Use a spatula to fold the wet and dry ingredients together just until combined (a few small lumps are fine).
- Don’t overfill the muffin cups: Fill each cup about 3/4 full so the muffins rise nicely without overflowing.
- Check doneness properly: Insert a toothpick into the centre. It should come out clean or with a few crumbs. If it’s still wet, bake for another minute or two.
- Add extra chocolate chips on top: It makes the muffins look bakery-style and ensures you get chocolate in every bite!
- Let them cool before removing: Allow the muffins to sit in the pan for 5–10 minutes after baking so they set before transferring to a rack.
Frequently Asked Questions
Yes. If you don’t want to use oat flour you can substitute it with equal parts of all-purpose flour like I use in this Pumpkin Banana Bread.
No I don’t recommend it. Pumpkin pie filling is filled with sugars and spices and will effect the taste of the muffins.
Try These Muffin Recipes Next!
Breakfast
Almond Flour Banana Muffins
Breakfast
Blueberry Cottage Cheese Muffins
Breakfast
Healthy Lemon Poppy Seed Muffins
Desserts
Healthy Gingerbread Muffins
If you tried these Healthy Pumpkin Muffins or any other recipe on the blog let me know how you liked it by leaving a comment/rating below! Be sure to follow along on Pinterest, Instagram and Facebook for even more deliciousness!
Healthy Pumpkin Muffins
- Prep Time: 10 minutes
- Cook Time: 20 minutes
- Total Time: 30 minutes
- Yield: 12 muffins
- Category: Breakfast, Dessert
- Method: Bake
- Cuisine: American
- Diet: Vegetarian
Description
These Healthy Pumpkin Muffins with chocolate chips are light, fluffy and made with oat flour for a healthier whole-grain twist!
Ingredients
- 1 1/2 cups oat flour
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/4 tsp salt
- 1 1/2 tsp pumpkin pie spice
- 2 large eggs
- 1/2 cup pure maple syrup
- 1/2 cup avocado oil (or melted and cooled butter)
- 1/4 cup milk of choice
- 1 cup pure pumpkin purée
- 2 tsp vanilla extract
- 1/2 cup mini chocolate chips (plus more for topping)
Instructions
- Preheat the oven to 350°F (180°C) and line a muffin pan with paper liners.
- In a medium bowl, whisk together the oat flour, baking powder, baking soda, salt, and pumpkin pie spice.
- In a separate large bowl, whisk together the eggs, maple syrup, avocado oil, milk, pumpkin purée, and vanilla extract until smooth.
- Pour the dry ingredients into the wet ingredients and use a spatula to gently fold everything together until just combined.
- Stir in the chocolate chips. Be careful not to overmix.
- Divide the batter evenly between the muffin cups, filling each about 3/4 full. Sprinkle a few extra chocolate chips on top if desired.
- Bake for 18–22 minutes, or until a toothpick inserted in the centre comes out clean.
- Let the muffins cool in the pan for 5–10 minutes, then transfer to a wire rack to cool completely before serving.
Notes
- Use 100% pumpkin purée, not pumpkin pie filling.
- Mix gently. Overmixing makes muffins dense.
- Check doneness with a toothpick, it should come out clean or with a few crumbs.
- Make homemade oat flour by blending rolled oats until fine.
- No pumpkin spice? Mix 1 tsp cinnamon, 1/4 tsp nutmeg, 1/4 tsp ginger, and a pinch of cloves.
Nutrition
- Serving Size: 1 muffin
- Calories: 200
- Sugar: 12g
- Sodium: 160mg
- Fat: 11g
- Saturated Fat: 3g
- Carbohydrates: 21g
- Fiber: 2g
- Protein: 4g
I double the recipe and added 1/4 cup of brown sugar, some extra ground glove, put in a little ground ginger to bring out the spices. Flavor was great. I did have some issues with the muffins deflating a bit. I haven’t worked with gf flour options. I spooned it in rather than packing like ap four. Is this different in gf flours? Do you know why they deflated?
Hi Lauren, i’m glad you enjoyed the recipe! Did you use a 1-1 gluten-free flour? Or did you use oat flour? This can also happen from overmixing the batter, if you take them out of the oven too early (You should always test that a toothpick comes out clean, since different ovens can have slight variances in temperature) Hope this helps!
They turned out excellent, this one will be on repoeat for certain.
Happy you enjoyed them!
I saw this recipe and I’m not a big fan of chocolate in muffins. I was pleasantly surprised how tasty they turned out with pumpkin + spice+ chocolate. Truly a winning combination! The recipe was so easy and the muffins had a great texture. Well done Jessica! I’ll be looking forward to my next attempt at a Choosing Chia recipe!
So glad you enjoyed it Robin!
Very good – added the walnuts & cocoa powder – thank you
Glad you enjoyed them!
These are delicious ! Toddler and adult approved. Friends that we shared them with also loved them.
Making these now! SO excited 😀
Could I use 2 flax eggs instead of eggs?
Hi April, I haven’t tested out this recipe myself with a flax egg so I couldn’t say for sure. If you test it out please let me know!
I made these today with GF flour and 2 flax eggs- they are amazing! I never have good luck with GF/egg free baking – still learning- but these were very easy and I really can’t believe how good they turned out!! (because of the baker- not the recipe!)
Also my muffin tins must be very small – I got 30 muffins 🙂
Hi Catherine, so happy this recipe turned out well for you!