When I posted these Healthy Pumpkin Cookies last week, I was hesitant to fully embrace pumpkin season and the thicker sweaters that come with it. Buuuuut after I shopped ransacked Trader Joe’s, where the festive fall foods were out in full form (check my Instagram “Favorites” highlight for the haul), I went from pumpkin prudent to pumpkin palooza. Fall baking, here we come! These tender muffins are sweetened naturally with honey or maple syrup. I also added oats for their homey flavor and subtle texture. Since pumpkin can be bland on its own, I made sure to be generous with the warm spices that are critical to bringing out its quintessential taste: cinnamon, nutmeg, ginger, and allspice ensure these muffins are bursting with fall flavor. If you are the kind of person who lives for the smell of pumpkin spice and harvest-scented candles, you are going to adore the way your kitchen smells as these (or my Pumpkin Scones) bake!

In Search of the Best Healthy Pumpkin Muffins

This recipe began as an innocent adaptation of my one-bowl Healthy Pumpkin Bread. I had been craving pumpkin oatmeal muffins so I thought, “Great! I’ll just swap out some of the flour in the pumpkin bread for oatmeal, bake the batter in a muffin pan instead, and we’ll be in breakfast heaven before I know it.” NOPE. It turns out that one of the things I adore most about baking with pumpkin—its natural moisture makes it ideal for creating healthy versions of my favorite snacks and treats—also means that nailing the right ratio of dry and wet ingredients isn’t, well, cut-and-dried. All-in-all, it took me four attempts to get these muffins just right (I thought I had it after the third, then did one more tweak for verification purposes). It was worth it! Combine the benefits of pumpkin itself (see more in “Healthy Baking with Pumpkin” below) with the fact that these muffins are 100% whole grain and naturally sweetened with honey, and you have a wholesome recipe for fluffy muffins that you can feel good enjoying regularly for healthy breakfasts and snacks.

Healthy Baking with Pumpkin

When you choose your ingredients thoughtfully, pumpkin muffins are one of the healthiest types of muffins to bake.

Canned pumpkin is packed with fiber, potassium, iron, and Vitamin A (which is important for boosting your immune system), as well as a number of healthy antioxidants. You can read about the additional benefits of pumpkin here.Since pumpkin is so moist, it can stand in for oil and butter used in many recipes (pumpkin is a common healthy baking substitute for oil and eggs). In fact, this recipe only requires two tablespoons of oil. This helps lessen the overall calories.Pumpkin’s flavor is not overwhelming, so it allows the recipe’s other flavors to shine. You can get away with a lesser amount of honey or maple syrup to naturally sweeten these muffins. (This Pumpkin Banana Bread is another of my favorite recipes that leverages natural sweetness).

PSSST!!! If you love healthy baking, I promise it’s worth getting a copy of The Well Plated Cookbook, which has muffins and many other healthy baked goods inside!

How to Make Healthy Pumpkin Muffins from Scratch

At their heart, these healthy pumpkin muffins with yogurt are meant to be a healthy breakfast item or snack. That way you don’t have to feel guilty devouring a healthy pumpkin oatmeal muffin mid-afternoon. (Though if you are looking for a sweeter pumpkin recipe to serve as dessert, try my one-bowl Pumpkin Sheet Cake with Greek Yogurt Cream Cheese Frosting.) This recipe is incredibly easy if you’re tight on time or don’t want to make a messy kitchen. All of the batter whips up in one bowl with a spatula (which was a major blessing throughout all of my recipe testing!).

The Ingredients

Pumpkin. Fall happiness + plenty of health (see above). This recipe calls for one whole can of pumpkin, so you don’t have to waste any amount of an opened can.Greek Yogurt. Provides additional moisture and creates a fluffy, exceptionally moist muffin—not the typical dense muffin that can result from using 100% whole grain.Oatmeal + Whole Wheat Flour. Wholesome, fiber-packed additions that give these muffins a delightfully nutty flavor.Honey. To keep these muffins free from refined sugar, I sweetened them with honey (maple syrup would also work beautifully here). The honey tastes wonderful with the spices, oats, and pumpkin too.Spices. Cinnamon, nutmeg, ginger, and allspice make these muffins instantly warm and cozy. They’re essential for bringing out the perfect pumpkin flavor.

The Directions

Healthy Pumpkin Recipe Adaptations

If you’ve made Well Plated recipes before, you’ll likely know one of my go-to healthy swaps is often using applesauce in place of butter and oil. Here, however, I do not recommend making healthy pumpkin muffins with applesauce in place of the oil. The pumpkin already contributes scrumptious moisture, so adding applesauce in addition to the pumpkin and Greek yogurt would most likely make the muffins too mushy. These are tried and true recipe adaptations you can enjoy instead:

Gluten Free. Baking pumpkin muffins with almond flour is an excellent option to make healthy pumpkin muffins gluten free. Check out this recipe Almond Flour Pumpkin Muffins. You also can follow this recipe, but swap in a 1:1 baking blend for the wheat flour.Vegan. My Vegan Pumpkin Muffins are a perfect fit for what you’re craving!Chocolate Chips. To make healthy pumpkin muffins with chocolate chips, add 2/3 cup of your favorite chocolate chips to the batter. Or for a similar taste and texture with oats too, you’ll devour this Healthy Pumpkin Chocolate Chip Bread.

Storage Tips

To Store. Since these healthy pumpkin muffins are so moist, I recommend storing them in the refrigerator in a paper towel-lined airtight storage container for up to 4 days. The pumpkin flavor becomes even more pronounced on day 2.To Freeze. Freeze muffins in an airtight freezer-safe storage container for up to 3 months. Thaw and enjoy as desired (I like to individually wrap my muffins so I can grab them for quick breakfasts and snacks).

More Healthy Ways to Bake with Pumpkin

Vegan Pumpkin BreadPumpkin Maple Coffee CakePaleo Pumpkin BreadPumpkin Oatmeal CookiesPumpkin Snickerdoodles

Muffin Pan. With this tool, you can whip up any of my healthy muffins at any time.Mixing Bowls. These are stackable and dishwasher- and microwave-safe.Measuring Spoons. Perfect for recipes that require you to measure lots of spices.

Do you have a favorite healthy way to bake with pumpkin? I’m fully stocked and ready to live my best pumpkin spice kind of life! If you try this recipe, please comment below and let me know how it turned out! I love hearing from you.

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