These Pumpkin and Apple Muffins with Raisin and Pepitas are made with pumpkin puree, diced apple, plump raisins, and crunchy pepitas folded into a warmly spiced batter.

Two fall flavors in one muffin, with enough texture from the seeds and raisins that they don’t need any glaze or streusel on top.

I make these on the weekend when the house could use that baked-pumpkin smell, and they freeze well enough that I usually double the batch.

They’re a good grab-and-go breakfast, or an afternoon snack with coffee.

If pumpkin and apple baking is your thing this time of year, try these recipes:

Pumpkin and Apple Muffins with Raisin and Pepitas

Ingredients You’ll Need

Canned pumpkin puree keeps these muffins moist without adding much extra prep (just make sure it’s pure pumpkin, not pumpkin pie filling, which already has sugar and spices mixed in).

Pepitas add a nice crunch against the soft crumb, and a small handful saved for the tops gives the muffins a little texture before they even go in the oven.

Ingredients

1 3/4 cups all-purpose flour
1 teaspoon baking soda
1/2 teaspoon baking powder
2 teaspoons pumpkin pie spice
1/4 teaspoon salt
1 cup pumpkin puree
2 large eggs
1/2 cup vegetable oil
3/4 cup brown sugar, packed
1/4 cup granulated sugar
1 teaspoon vanilla extract
1 cup apple, peeled and diced small
1/2 cup raisins
1/3 cup pepitas, plus extra for topping

Directions

Preheat the oven to 375°F and line a 12-cup muffin tin with paper liners.
In a medium bowl, whisk together the flour, baking soda, baking powder, pumpkin pie spice, and salt.
Set this aside.
In a large bowl, whisk the pumpkin puree, eggs, vegetable oil, brown sugar, granulated sugar, and vanilla extract until smooth.
It should look thick and glossy, more like a batter than a liquid at this point.
Add the dry ingredients to the wet ingredients and stir just until combined.
Some streaks of flour disappearing into the batter is fine, just don’t keep stirring past that point or the muffins turn dense.
Fold in the diced apple, raisins, and pepitas with a spatula, distributing them evenly through the batter.
This part takes a minute since the batter is thick, but resist the urge to overmix while you’re folding.
Divide the batter evenly among the muffin cups, filling each about three-quarters full.
Sprinkle a few extra pepitas over the top of each one before baking.
Bake for 20 to 22 minutes, until a toothpick inserted in the center comes out clean.
Check at the 20-minute mark. Pumpkin batter can look done on top before the center fully sets, so give it the toothpick test rather than judging by color alone.
Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Serve warm or at room temperature and enjoy!

Important Recipe Notes

Use pure pumpkin puree. Double-check the can says 100% pumpkin, not pumpkin pie filling. The filling version already has added sugar and spices, which throws off the whole recipe.
Dice the apple small. Small pieces distribute more evenly through the batter and cook through fully in the bake time. Large chunks can stay a little firm in the center.
Don’t overmix once the apple goes in. Fold gently just until everything is distributed. Overworking the batter at this stage is the most common reason these turn out tough instead of tender.

Toast the pepitas first for more flavor. This step is optional, but a quick 3 to 4 minute toast in a dry skillet brings out a nuttier flavor in the pepitas before folding them in.
Storage. Store cooled muffins in an airtight container at room temperature for up to 3 days, or in the fridge for up to a week.
Freezing. These freeze well for up to 3 months. Wrap individually and thaw at room temperature, or warm in the microwave for 20 to 30 seconds.
This batch takes a little longer than a basic muffin. Between the dicing, folding, and toasting the pepitas if you go that route, it’s not a five-minute recipe, just so you know going in.

How to Serve, Store & Customize This Recipe

Serving:

Serve these warm or at room temperature, with a smear of butter if you want it.

They’re substantial enough to work as a full breakfast alongside a cup of coffee or a glass of milk.

Storage:

Keep muffins in an airtight container at room temperature for up to 3 days. In the fridge, they’ll keep for about a week, though the texture is best within the first few days.

They freeze well individually wrapped for up to 3 months.

Customization:

Swap the raisins for dried cranberries for more tartness, or leave them out entirely if you’re not a fan.

Chopped pecans or walnuts work in place of the pepitas. For a spicier muffin, add an extra half teaspoon of pumpkin pie spice or a pinch of ground ginger.