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Preheat oven to 375F. Line 12 muffin cups with paper liners.
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To make the cream cheese filling, use an electric mixer to beat together cream cheese, brown sugar, and maple syrup. Set aside.
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To make the muffins, beat together vegetable oil, brown sugar, pumpkin, maple syrup, eggs, and vanilla until well combined.
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In a separate bowl, whisk together flour, baking powder, baking soda, cinnamon, and salt until no lumps remain. Add this mixture to the wet ingredients and stir until just combined.
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Put about a tablespoon of the batter in the bottom of each muffin cup (enough to cover the bottom well). Place a heaping teaspoon of the cream cheese mixture on top in each cup. Divide remaining mixture among the muffin cups.
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In a small bowl, combine raw sugar and pumpkin seeds. Sprinkle over batter.
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Bake 22 - 24 minutes or until a toothpick inserted into the center of the muffin comes out clean.
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Cool completely on a wire rack before serving.