Gluten free pumpkin spice cream cheese muffin recipe

These gluten free pumpkin cream cheese muffins use Philly pumpkin cream cheese as an easy filling, and are garnished with pumpkin seeds.

These gluten free pumpkin cream cheese muffins use Philly pumpkin cream cheese as an easy filling, and are garnished with pumpkin seeds.

To be perfectly honest, I can’t remember if I ever ate a “real” Starbucks pumpkin cream cheese muffin, before I had to start eating gluten free in the year 2000. But they look so yummy. I’ve been experimenting with adapting gluten free versions of the recipe for several years. Then I saw the Philly pumpkin spice cream cheese at the grocery store, and inspiration struck!

Most cream cheese fillings are a separate step involving an egg, sugar, flavorings, and dirtying an extra bowl. I had a theory that the pumpkin spice cream cheese would streamline the process, and the dishes. It worked, and they were delicious! The muffins were a hit with gluten free folks and gluten eaters alike when I brought them to a family event later that day.

Dairy-free, vegan variations: To make these muffins dairy free, you could just skip the cream cheese filling (since the muffins are moist and flavorful all on their own). Or you could create a “cream cheese” filling by mixing 4 oz. of the dairy free “cream cheese” of your choice with 1 ½ TBS sugar and 1 egg. Or to make them completely vegan, just skip the egg, or sub in 2 TBS applesauce to loosen up the mixture.

Some recipes call for a sprinkling of chopped nuts (pecans, or walnuts are most common), but I prefer pumpkin seeds on these muffins. They have the bonus of being more allergy friendly, and have the obvious pumpkin flavor connection. Although I have used pecans, and they were delicious too.

* Note: I’ve included a few links to affiliate products that I use and love.

Recipe for gluten free pumpkin spice cream cheese muffins

Makes 12 muffins

Preheat oven to 350 degrees F

Total time: 35 minutes

Prepare muffin tins (with paper liners, or greased with vegetable oil spray)


1 ½ cups Krusteaz gluten free flour blend (you could use a cup-for-cup gluten free flour blend of your choice, but your results might vary)

4 teaspoons pumpkin pie spice

1 pinch ground cardamom (optional)

1/2 teaspoon salt

1 teaspoon baking soda

2 eggs

1 cup sugar

1 cup pumpkin puree

⅔  cups vegetable oil

4 ounces of pumpkin cream cheese

¼ cup pumpkin seeds


  1. In a large bowl, whisk together the dry ingredients: Gluten free flour mix, pumpkin pie spice, cardamom (if using), salt, and baking soda.

  2. In a separate medium sized bowl, or large 4-cup liquid measuring cup, mix together the eggs, sugar, pumpkin, and oil.

  3. Fill prepared muffin tins 2/3 full. (A regular sized scoop with trigger release is perfect for this job.)

  4. Put 2 tsp. pumpkin cream cheese or “cream cheese” mixture in the middle of each muffin, pressing down slightly. (A small trigger scoop is a helpful tool for this task).

  5. Sprinkle a few pumpkin seeds on each muffin, (of if you’re like me, carefully count out and arrange 3 seeds on each muffin).

  6. Bake at 350 for 25 minutes, until they are deep golden brown (do not underbake).

  7. Let the muffins cool in the pans for 5 minutes, then carefully put them on cooling racks to cool completely. I know it’s tempting, but don’t touch the cream cheese until it cools, unless you want burnt fingers.

Enjoy! The muffins will keep, covered, at room temperature for 3-4 days. The cream cheese filling and vegetable oil help keep them nice and moist. You can wrap them individually in plastic wrap and then put them in a freezer bag in the freezer. Don’t store gluten free baked goods in the refrigerator - it dries them out and makes them crumbly