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Soft, fluffy, and full of cozy fall flavor – these healthy pumpkin muffins are naturally sweetened with maple syrup and made with simple, wholesome ingredients. They’re gluten-free, dairy-free, and refined sugar-free, but taste just as indulgent as a bakery muffin.
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Why You’ll Love These Healthy Pumpkin Muffins
These pumpkin muffins are healthy, naturally sweetened, gluten-free, and dairy-free, but you’d never guess it from how soft and flavorful they are.
I wanted a muffin that felt cozy and indulgent, without refined sugar or heavy ingredients, and after a few test batches, this one hit the mark.
They’re tender and moist, perfectly spiced, with just the right amount of sweetness from maple syrup. You can enjoy them as-is, add chocolate chips or dress them up with a sprinkle of cinnamon sugar (both totally optional, but so good!).
These muffins are everything I love about cozy fall baking – warm spices and that sweet pumpkin aroma filling the kitchen. They’ve quickly become one of my fall baking favorites, and I can’t wait for you to try them.
RELATED: For more gluten-free muffin recipes, check out these Banana Nut Chocolate Chip Muffins.
What You’ll Need
These pumpkin muffins are simple, cozy, and come together with pantry staples. I’ve baked them multiple times – they never fail to be tender, flavorful, and just sweet enough.
- Pumpkin puree – Be sure to use 100% canned pure pumpkin puree, not pumpkin pie filling.
- Coconut oil – Keeps the muffins moist. Extra light olive oil or neutral oil also work.
- Pure maple syrup – Adds natural sweetness and depth.
- Eggs – Bind everything together and help the muffins rise.
- Vanilla extract – Adds that warm, homey flavor.
- Flour – I like to use a 1:1 gluten-free flour but all-purpose flour works beautifully too.
- Baking powder & baking soda – For lift and light texture.
- Salt – Balances the sweetness.
- Pumpkin pie spice – The cozy heart of the recipe. If you don’t have any on hand, you can easily make your own! Just mix 1 teaspoon cinnamon, ¼ teaspoon nutmeg, ¼ teaspoon ginger, and a pinch of cloves or allspice.
- Optional mix-ins – Chocolate chips, chopped pecans, or a sprinkle of cinnamon sugar on top before baking. I sometimes make them with cinnamon sugar and sometimes with chocolate chips – honestly, both versions disappear fast!
For a full ingredients list with measurements, check the recipe card below.
How to Make Healthy Pumpkin Muffins
- Prep the pan and oven. Preheat your oven to 350 F and line a 12-cup muffin tin with paper baking cups.
- Stir together the wet ingredients. In a large bowl, stir together the pumpkin puree, melted coconut oil, eggs, maple syrup, and vanilla until everything looks smooth and well combined.
- Mix the dry ingredients. In a separate bowl, mix together the flour, baking powder, baking soda, salt, and pumpkin pie spice.
- Combine wet and dry, and add mix-ins. Fold dry ingredients into the wet ingredients and stir gently until just combined. The batter should be thick but smooth, don’t overmix. Fold in mix-ins, if using.
- Fill the muffin pan. Divide the batter evenly among the 12 muffin cups, filling each about ¾ full. (Keep them simple, or add your favorite mix-ins – check out the “Variations” section for inspiration!)
- Bake and enjoy! Bake for 20–22 minutes, or until a toothpick inserted in the center comes out clean. Let the muffins cool in the pan for a few minutes, then transfer & cool on a wire rack. Serve warm or at room temperature!
TIPS FROM NELI’S KITCHEN
Baker’s Notes & Pro Tips
Here are some tips to ensure your gluten-free Pumpkin Muffins turn out perfect every time:
- Don’t overmix the batter. Once the wet and dry ingredients come together, stir just until you don’t see streaks of flour. Overmixing can make your muffins dense instead of soft and fluffy.
- Use room temp ingredients. If your pumpkin puree or eggs are cold, the melted coconut oil can harden in the batter. I like to let the eggs sit out for 10 minutes before starting.
- Fill each muffin cup about ¾ full. This gives you that perfect dome shape – full, round tops without overflowing.
- Check for doneness early. Ovens vary, so start checking around 20 minutes. A toothpick should come out clean or with a few moist crumbs.
- Cool before removing. Let the muffins rest in the pan for 5–10 minutes before transferring to a rack. It helps them set and keeps the bottoms from getting soggy.
- Mix-in magic. I love these healthy pumpkin muffins several ways – topped with cinnamon sugar for a cozy crunch or loaded with chocolate chips for a sweet treat. Both versions are hits in my house!
- Make-ahead friendly. These freeze beautifully. I often tuck a few into the freezer and warm them in the toaster oven. They taste freshly baked every time.
Easy Variations to Try
These gluten-free pumpkin muffins never last long in my kitchen, and I have to admit, that cinnamon sugar topping might just be my current favorite!
- Cinnamon Sugar Crunch – Sprinkle a little cinnamon sugar on top before baking for a sweet, sparkly finish.
- Chocolate Chip Treat – Stir in a handful of chocolate chips for a dessert-like version (another personal favorite when I’m craving a chocolatey fall treat).
- Nutty Pumpkin – Add chopped pecans or walnuts for a lovely crunch.
- Pumpkin Cranberry – Fold in dried cranberries for a tangy, festive twist.
- Streusel Topping – Mix 2 tablespoons butter, 2 tablespoons brown sugar (or coconut sugar), and 2 tablespoons flour with a pinch of cinnamon until crumbly, then sprinkle over each muffin before baking. It adds a bakery-style crunch and just a hint of sweetness on top.
- Mini Muffins – Bake in a mini muffin tin for about 12–14 minutes – perfect for snacks or lunchboxes.
Storing & Reheating
These maple pumpkin muffins keep beautifully! I often bake a double batch for an easy grab-and-go snack for the busy school week or afternoon coffee breaks.
- Room temperature – Store in an airtight container for up to 3 days. I like to line the container with a paper towel to absorb a little extra moisture.
- Fridge – For longer storage, refrigerate for up to 5 days. I’ve noticed they firm up a bit after being in the fridge (probably because of the coconut oil) but once they warm up or come to room temp, they’re soft again.
- Freezer – Freeze for up to 2 months in a freezer bag or container. I love keeping a stash on hand, they’re one of my favorite make-ahead muffins for healthy fall snacks.
To reheat – Pop one in the microwave for about 20 seconds, or warm in a 300 F oven for 5–7 minutes. They taste just like fresh-baked again – especially with a pat of butter or drizzle of maple syrup.
More Fall Desserts To Try
If you love this easy pumpkin muffin recipe, here are a few more reader-favorite recipes to keep that cozy fall baking going:
Breakfast Recipes
Cranberry Orange Muffins
Desserts
Pumpkin Cake
Breakfast Recipes
Healthy Apple Muffins
Desserts
Applesauce Cake
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Healthy Pumpkin Muffins
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Ingredients
- 1 cup canned pumpkin puree
- ½ cup coconut oil, melted
- 2 large eggs
- ¾ cup maple syrup
- 1 teaspoon vanilla extract
- 1½ cups all-purpose flour, or gluten-free flour if preferred
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- 2 teaspoons pumpkin pie spice
- Optional mix-ins: 1 cup chocolate chips or chopped pecans
- Optional topping: cinnamon sugar topping, 1 Tbsp sugar mixed with 1 tsp cinnamon
Instructions
- Preheat oven to 350 F and line a 12-cup muffin tin with paper liners.
- In a large bowl, stir together the pumpkin puree, melted coconut oil, eggs, maple syrup, and vanilla until smooth.
- In a separate bowl, mix together the flour, baking powder, baking soda, salt, and pumpkin pie spice.
- Add the dry ingredients to the wet ingredients and stir just until combined and no flour streaks remain. Fold in chocolate chips or pecans if using.
- Divide the batter evenly among the muffin cups, filling each about ¾ full. Sprinkle cinnamon sugar on top if using.
- Bake for 20–22 minutes, or until a toothpick inserted in the center comes out clean. Cool slightly before serving and enjoy!
Notes
- Don’t overmix the batter. Once the wet and dry ingredients come together, stir just until you don’t see streaks of flour. Overmixing can make your muffins dense instead of soft and fluffy.
- Use room temp ingredients. If your pumpkin puree or eggs are cold, the melted coconut oil can harden in the batter. I like to let the eggs sit out for 10 minutes before starting.
- Fill each muffin cup about ¾ full. This gives you that perfect dome shape – full, round tops without overflowing.
- Check for doneness early. Ovens vary, so start checking around 20 minutes. A toothpick should come out clean or with a few moist crumbs.
- Cool before removing. Let the muffins rest in the pan for 5–10 minutes before transferring to a rack. It helps them set and keeps the bottoms from getting soggy.
- Mix-in magic. I love these healthy pumpkin muffins several ways – topped with cinnamon sugar for a cozy crunch or loaded with chocolate chips for a sweet treat. Both versions are hits in my house!
- Make-ahead friendly. These freeze beautifully. I often tuck a few into the freezer and warm them in the toaster oven. They taste freshly baked every time.
Nutrition
Nutrition Disclaimer: Nutritional values are estimates and may vary with ingredients, brands, and portion sizes. For accuracy, use your preferred nutrition calculator.
Disclaimer: The information provided in this recipe is for informational purposes only and should not be considered medical or nutritional advice. I am not a doctor or a dietitian. Always consult a qualified healthcare provider for personalized guidance regarding your diet or health. For more details, please read my full disclosure page.
