Name: Healthier Pumpkin Cream Cheese Muffins
Prep time: 15 min
Cook time: 20 min
Total time: 35 min
Cuisine: American
Ingredients: 1 3/4 cups whole wheat flour; 1 teaspoon baking soda; 1 1/2 teaspoons pumpkin pie spice (or a blend of cinnamon, nutmeg, and cloves); 1/4 teaspoon salt; 1 cup pumpkin purée (unsweetened); 1/2 cup maple syrup or honey; 1/3 cup melted coconut oil or avocado oil; 2 large eggs; 1 teaspoon vanilla extract; 2–3 tablespoons Greek yogurt (optional); 4 oz light cream cheese; 1 teaspoon maple syrup or 1/2 teaspoon vanilla extract (for cream cheese mixture); Coconut sugar or brown sugar (for sprinkling)

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Healthier Pumpkin Cream Cheese Muffins are a wholesome twist on the classic fall favorite. With warm spices, real pumpkin, and a creamy tangy center, these muffins satisfy my sweet tooth while using better-for-you ingredients like whole wheat flour, natural sweeteners, and light cream cheese.

Why You’ll Love This Recipe

I love how these muffins feel indulgent without being overly heavy. They’re made with nutrient-rich pumpkin, lower sugar, and healthier fats, so I can enjoy them any time of day without guilt. The cream cheese center adds a luscious surprise in every bite, and the blend of cinnamon, nutmeg, and cloves makes my kitchen smell amazing. They also freeze well, so I keep them on hand for busy mornings or cozy snacks. Healthier Pumpkin Cream Cheese Muffins

Ingredients

(Here’s a tip: Check out the full list of ingredients and measurements in the recipe card below.)

Whole wheat flour
Baking soda
Pumpkin pie spice (or a blend of cinnamon, nutmeg, and cloves)
Salt
Pumpkin purée (unsweetened)
Maple syrup or honey
Coconut oil (melted) or avocado oil
Eggs
Vanilla extract
Light cream cheese
Greek yogurt (optional, for extra moisture)
Coconut sugar or brown sugar (for sprinkling)

Directions

I preheat the oven to 350°F (175°C) and line a muffin tin with paper liners or lightly grease it.
In one bowl, I whisk together the dry ingredients: whole wheat flour, baking soda, pumpkin spice, and salt.
In another bowl, I combine the pumpkin purée, maple syrup (or honey), melted coconut oil, eggs, and vanilla. I mix until smooth.
I gradually add the dry ingredients to the wet, stirring until just combined. If I want extra moisture, I mix in a spoonful of Greek yogurt.
In a separate small bowl, I beat the light cream cheese with a touch of maple syrup or vanilla until smooth.
I fill each muffin cup halfway with the pumpkin batter, then add about a teaspoon of the cream cheese mixture in the center.
I top each one with more batter until the cups are about ¾ full. If I’m feeling fancy, I sprinkle the tops with a little coconut sugar or brown sugar for crunch.
I bake the muffins for 18–22 minutes, until a toothpick inserted around the edge (not through the cream cheese) comes out clean.
I let them cool in the tin for 5 minutes before transferring to a wire rack.

Servings and timing

This recipe makes about 12 standard muffins. I spend around 15 minutes prepping, and baking takes about 20 minutes, so I usually have them ready in about 35 minutes total.

Variations

Sometimes I mix in chopped walnuts or pecans for crunch. I’ve also added dark chocolate chips to the batter for a more decadent version. For a dairy-free option, I use a vegan cream cheese alternative and skip the Greek yogurt. I also occasionally swap the pumpkin for mashed sweet potato or butternut squash for a subtle flavor change.

Storage/reheating

I store the muffins in an airtight container at room temperature for up to 2 days or refrigerate them for up to 5 days. I reheat them in the microwave for about 15 seconds to bring back that fresh-from-the-oven softness. If I make a big batch, I freeze the muffins individually and thaw them overnight or warm them up directly from frozen. Healthier Pumpkin Cream Cheese Muffins

FAQs

Can I use canned pumpkin pie filling instead of purée?

No, I stick with pure pumpkin purée. Pumpkin pie filling has added sugar and spices, which can throw off the flavor and sweetness of the muffins.

How do I keep the cream cheese from sinking?

I make sure the batter is thick and that I only press the cream cheese gently into the center. Adding more batter on top helps keep it nestled in the middle.

Are these muffins freezer-friendly?

Yes, I freeze them in a single layer first, then transfer to a freezer bag. They keep well for up to 2 months, and I reheat them in the microwave or let them thaw overnight.

Can I make these gluten-free?

I’ve tried using a 1:1 gluten-free flour blend with success. I just make sure it includes xanthan gum for structure.

What’s the best way to sweeten them naturally?

I like using pure maple syrup or honey as the main sweetener. Coconut sugar also works great for a deeper, caramel-like flavor.

Conclusion

These Healthier Pumpkin Cream Cheese Muffins strike the perfect balance between cozy and nutritious. I love how they offer all the classic fall flavors with a better-for-me ingredient list. Whether I grab one for breakfast, pack it as a snack, or serve it with tea, these muffins never disappoint.