High-Fiber Pumpkin Spice Cupcakes with Light Cream Cheese Swirl – Cozy Flavor with a Better-For-You Twist

Pumpkin spice and cream cheese are a classic pair, but these cupcakes bring extra fiber and a lighter swirl that won’t weigh you down. They’re tender, warmly spiced, and just sweet enough to feel special. The cream cheese swirl bakes right into the top, so you get a pretty marbled look without extra frosting.

Great for fall gatherings, lunchbox treats, or a cozy weeknight dessert. If you like comfort baking with a health-conscious angle, this recipe hits the sweet spot.

Why This Recipe Works

These cupcakes use a blend of white whole wheat flour and oat flour to pack in fiber while staying soft. Pumpkin puree adds moisture and flavor, so you can cut back on fat without sacrificing tenderness.

A touch of applesauce helps keep them fluffy and light. The cream cheese swirl is sweetened and thinned so it bakes into the top instead of sinking. You get that cheesecake vibe without a heavy frosting layer.

What You’ll Need

• Dry Ingredients
  • 1 cup white whole wheat flour
  • 3/4 cup oat flour (store-bought or finely ground oats)
  • 1 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon fine sea salt
  • 2 teaspoons pumpkin pie spice
  • 1/2 teaspoon ground cinnamon (optional for extra warmth)
• Wet Ingredients
  • 1 cup canned pumpkin puree (not pie filling)
  • 2 large eggs, room temperature
  • 1/2 cup light brown sugar, packed
  • 1/4 cup maple syrup or honey
  • 1/3 cup unsweetened applesauce
  • 1/4 cup neutral oil (avocado, grapeseed, or canola)
  • 1 teaspoon pure vanilla extract
  • 2 tablespoons milk (dairy or unsweetened plant milk)
• Light Cream Cheese Swirl
  • 6 ounces reduced-fat cream cheese (Neufchâtel), softened
  • 2 tablespoons plain Greek yogurt (2% or 0%)
  • 2–3 tablespoons powdered sugar, to taste
  • 1 teaspoon vanilla extract
  • Pinch of salt
• Optional Add-Ins
  • 1/2 cup finely chopped pecans or walnuts
  • 1/3 cup mini dark chocolate chips
  • 2 tablespoons ground flaxseed for extra fiber
• Tools
  • 12-cup muffin tin + liners
  • Two mixing bowls
  • Hand whisk or mixer
  • Scoop or spoon for batter
  • Toothpick or small knife for swirling

How to Make It

1. Prep the pan and oven. Line a 12-cup muffin tin with paper liners.

   Preheat the oven to 350°F (175°C).

2. Mix the dry ingredients. In a large bowl, whisk white whole wheat flour, oat flour, baking powder, baking soda, salt, pumpkin pie spice, and cinnamon until well combined.
3. Whisk the wet ingredients. In a separate bowl, whisk pumpkin puree, eggs, brown sugar, maple syrup, applesauce, oil, vanilla, and milk until smooth.
4. Combine wet and dry. Pour the wet mixture into the dry. Stir gently with a spatula until just combined. If using nuts, chocolate chips, or flaxseed, fold them in now. Do not overmix.
5. Make the swirl. Beat softened cream cheese with Greek yogurt, powdered sugar, vanilla, and a pinch of salt until creamy and spreadable.

   It should be thick but spoonable; add a teaspoon of milk if needed.

6. Fill the liners. Divide cupcake batter evenly among the 12 liners, about two-thirds full.
7. Add the swirl. Spoon about a teaspoon of the cream cheese mixture on top of each cupcake. Use a toothpick or knife to gently swirl it into the batter, making a few figure eights. Keep the swirl mostly on the surface so it doesn’t sink.
8. Bake. Bake for 18–22 minutes, or until the cupcakes spring back lightly and a toothpick inserted into the cake (not the swirl) comes out clean.
9. Cool. Let cupcakes cool in the pan for 5 minutes, then transfer to a rack. Cool completely to set the swirl.
10. Serve. Enjoy as is, or dust lightly with cinnamon before serving.

Keeping It Fresh

Store cupcakes in an airtight container in the fridge for up to 5 days due to the cream cheese swirl.

For the best texture, let them sit at room temperature for 10–15 minutes before eating. You can also freeze them (well wrapped) for up to 2 months. Thaw overnight in the fridge or at room temperature for about an hour.

Benefits of This Recipe

• Higher fiber, better satisfaction: White whole wheat flour, oat flour, pumpkin, and optional flaxseed help keep you full longer.
• Lighter swirl: Reduced-fat cream cheese plus Greek yogurt delivers creamy tang with fewer calories than a full frosting.
• Balanced sweetness: A mix of brown sugar and maple gives warmth without being overly sweet.
• Moist without heavy oil: Pumpkin and applesauce keep the crumb tender while using less fat.
• Make-ahead friendly: They hold up well for snacks, breakfast, or dessert through the week.

Pitfalls to Watch Out For

• Overmixing the batter: This can make cupcakes tough.

  Stir just until the flour disappears.

• Swirl sinking: If the cream cheese is too thin or you push it too deep, it can sink. Keep it thick and mostly on top.
• Overbaking: These can dry out if left too long. Start checking at 18 minutes.
• Using pumpkin pie filling: It’s pre-sweetened and spiced and will throw off the recipe.

  Use plain pumpkin puree.

• Skipping cooling time: The swirl sets as it cools. Cutting in early can smear the top.

Alternatives

• Gluten-free: Use a 1:1 gluten-free all-purpose flour blend and certified GF oat flour. Add 1 tablespoon ground psyllium husk for structure if you have it.
• Dairy-free: Use dairy-free cream cheese and yogurt, and a plant milk.

  Flavor and texture remain very similar.

• No refined sugar: Replace brown sugar with coconut sugar and powdered sugar with a powdered coconut sugar substitute. Note: color will be slightly darker.
• Nut-free: Skip nuts; add pumpkin seeds or extra chocolate chips if desired.
• Extra protein: Swap 2 tablespoons of oat flour for unflavored whey or plant protein. Add 1–2 tablespoons extra milk if the batter feels too thick.

FAQ

Can I use all-purpose flour instead of white whole wheat?

Yes.

Use the same amount. The cupcakes will be slightly lighter in color and a bit less hearty, but still moist and delicious.

How do I make oat flour at home?

Blend rolled oats in a high-speed blender until very fine, then fluff and measure. One cup of rolled oats yields about 3/4 cup oat flour.

Why is my cream cheese swirl lumpy?

The cream cheese was likely too cold.

Soften it at room temperature and beat well before adding yogurt and sugar. A quick whisk after mixing smooths it out.

Can I bake this as a loaf or mini loaves?

Yes. For a standard 9×5-inch loaf, bake at 350°F for about 50–60 minutes, tenting with foil if browning too fast.

Swirl the cream cheese over the top before baking.

Do I have to use applesauce?

No. Replace with an extra 2 tablespoons oil and 2 tablespoons milk for a richer crumb. The fiber will be slightly lower.

What if I don’t have pumpkin pie spice?

Use 1 1/2 teaspoons cinnamon, 1/4 teaspoon nutmeg, 1/4 teaspoon ginger, and a pinch of cloves or allspice.

How do I know they’re done if the swirl is wet?

Test the cake portion just beside the swirl with a toothpick.

It should come out clean or with a few moist crumbs. The swirl will look glossy but set as it cools.

Final Thoughts

These High-Fiber Pumpkin Spice Cupcakes with Light Cream Cheese Swirl deliver cozy bakery flavor with a smarter ingredient list. They’re tender, gently sweet, and easy to make on a weeknight.

Keep a batch in the fridge for breakfasts, snacks, or dessert, and enjoy that pumpkin-spice comfort with a lighter touch.