Name: Healthy Pumpkin Muffins
Prep time: 15 min
Cook time: 20 min
Ingredients: 1¾ c white whole wheat flour; 1 tsp baking soda; ½ tsp salt; 2 tsp cinnamon; ½ tsp nutmeg; ¼ tsp allspice; ¼ tsp ginger; ¼ tsp pumpkin pie spice; 1 c pumpkin puree; 2 large eggs or flax eggs; ½ c maple syrup or date syrup (*see notes); ¼ c unsweetened applesauce; ¼ c unsweetened almond milk; 1 tsp vanilla extract; ½ tsp almond extract; ½ c walnuts, chopped ((optional)); ⅓ c dark, semi-sweet, or mini chocolate chips ((optional))

Jump to Recipe Print Recipe

These Healthy Pumpkin Muffins are the perfect way to bake your way into fall. These muffins are oil-free, naturally sweetened, incredibly moist, and surprisingly decadent. *Pairs well with a pumpkin latte. 😉

Healthy pumpkin muffins on a small cutting board with an orange napkin in the background.

We absolutely love the fall season. It’s the perfect baking season. The weather is cool and crisp (in my head…in reality it’s muggy and hotter than heck in Celina), it’s time to break out those boots and sweaters, and snuggle up with cozy scents and flavors.

Enter the best flavor of the season: pumpkin.

We are definitely pumpkin obsessed. When September first hits and Starbucks rolls out the PSL, you’d better believe we are first in line, even though the heat index is still like 150F. We like to think of the PSL as a good luck charm that brings fall to Texas. So far, it’s had a patchy run at best. 😅

If you’ve got pumpkin fever like us, make sure you check out our other pumpkin-inspired dishes, like energy bites, ramen, and even pesto!

Overhead shot of many healthy pumpkin muffins on orange napkin beside a bowl of walnuts.

Pumpkin Muffin Ingredients

Pumpkin – pumpkin puree is the key to this recipe. It lends plenty of pumpkin flavor, keeps these muffins moist, and gives them a boost in vitamins, minerals, and antioxidants.
Applesauce – unsweetened applesauce is a delicious and healthy substitute for oil in baked goods. Plus it gives an extra dose of natural sweetness that helps us cut back on added sugars in this recipe.
Maple or date syrup – these natural sweeteners are less processed and are much lower on the glycemic index than cane sugar, helping to pack in extra micronutrients that cane sugar lacks.
White whole wheat flour – when we can, we love to sneak in whole wheat flour into our baked goods. It is less processed than all-purpose flour and add a little extra fiber, protein, and vitamins and minerals to these muffins without affecting the flavor or texture.
Milk – we used unsweetened vanilla almond milk in this recipe. Feel free to sub in your favorite plant or animal milk, like cashew, hemp, oat, or cow’s milk.
Eggs – we use real eggs in this recipe, but if you want to keep this recipe vegan, swap for flax egg. Note that we have not made this recipe with flax eggs and cannot comment on how flax egg affects the flavor or texture.
Spices – these muffins are loaded up with fall spices that are normally found in pumpkin pie, like cinnamon, nutmeg, all-spice, ginger, and a little extra pumpkin pie spice.
Vanilla & almond extracts – we’re all familiar with the deliciousness of vanilla extract in baking, but we included almond extract for an unexpected sweet and nutty undertone.
Mix-ins (optional) – this recipe calls for chopped walnuts and dark chocolate chips. But feel free to omit or substitute with your favorite nuts, seeds, or chocolate. Or top with a cobbler crumble like we did in these apple cobbler muffins.

Healthy pumpkin muffins on a small cutting board with date syrup and napkin in the background.

How to Make Pumpkin Muffins

Preheat the oven to 350°F. Lightly grease a muffin pan with cooking spray or line with muffin tins/liners. Set aside.

Mix together the dry ingredients by combining the flour, baking soda, salt, cinnamon, nutmeg, allspice, ginger, and pumpkin pie spice in a large mixing bowl. Stir the ingredients loosely together and set aside.

Mix together wet ingredients by combining the pumpkin puree, eggs, maple syrup, applesauce, almond milk, vanilla extract, and almond extract in a medium mixing bowl.

Make a small well in the dry ingredients and pour the wet ingredients into the dry ingredients. Fold the wet ingredients into the dry ingredients, loosely incorporating. Be careful not to over-mix the batter (you should have a few light flour streaks). Fold in half of the walnuts and chocolate chips, if desired, and reserve the remainder for topping the muffins. This batter will be fairly thick.

Wet and dry ingredients incorporated with chocolate chips and walnuts not mixed in.

Scoop the muffin batter into the prepared muffin tins, filling ¾ full to completely full for more voluminous muffin tops. Sprinkle each muffin with the remaining walnuts and chocolate chips, if desired.

Bake 18 to 20 minutes, or until a toothpick comes out from the muffin center cleanly or with a few crumbs. Cool the muffins in the muffin pan on a cooling rack for 5 to 10 minutes before serving, or allow to cool completely before storing.

Twelve cooked muffins in the muffin pan.

Close view of pumpkin muffins in muffin pan.

Recipe tip: maple syrup is considerably sweeter than date syrup. If you use date syrup you may need to increase the amount to 2/3 to 3/4 cup in order to be of similar sweetness to maple syrup.

Close view of healthy pumpkin muffins in front of orange napkin and date syrup bottle.

How to Store Pumpkin Muffins

Room temperature – allow the muffins to cool completely before storing. Line a large airtight baggie with paper towel and store muffins in a single layer for up to 5 days. You can place an additional optional paper towel on top, if desired. The paper towel will help reduce the moisture content and prevent the muffins from getting too soggy.

Freezer – these muffins are freezer friendly. Allow the muffins to cool completely before storing. Add the muffins to a freezer-safe airtight baggie in a single layer. Remove as much air as possible from the bag before freezing. You can store these muffins in the freezer for up to 3 months! We recommend writing the date you put them in the freezer and the date they need to be eaten by for optimal freshness. When you’re ready to eat them, you can defrost the desired quantity overnight in the fridge. Or pop them into the microwave for a 20 to 30 seconds, until warmed throughout.

Let us know what you think about these Healthy Pumpkin Muffins by dropping a comment and/or rating below! Also, please share this recipe on Pinterest or social media if you enjoyed it (we greatly appreciate you sharing the love)! 💕

Check out our other fall-inspired bakes:

Also, a special thanks to D’Vash Organics for gifting us with the yummy date syrup we used in this recipe. We are big fans of natural sweeteners and felt that this brand aligned with our content and our users. However, we want to be clear that we received this syrup for free, in exchange for incorporating it into a recipe and sharing it with our users.