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Preheat oven to 400F. Line or grease a 12-cup muffin tin.
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To make the filling, microwave the cream cheese in a microwave safe bowl for about 40 seconds on low. Stir in sugar an vanilla. Set aside.
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Sift together flour, baking powder, baking soda, cinnamon, ginger, and salt. Set aside.
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In the bowl of a mixer, beat together the sugar, brown sugar, eggs, water, and vegetable oil until light. Slowly add in the dry ingredients and beat until just moistened. Add carrots and beat just a couple seconds until the carrots are dispersed.
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Put about 2 tablespoons of batter into each muffin cup. Add a heaping tablespoon into the center of each cup. Top with another couple tablespoons of batter, making sure the cream cheese is completely covered.
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Bake for about 20 minutes or until golden and a toothpick inserted into the center (of the actual muffin, not cream cheese) comes out clean. Cool completely on a wire rack.
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Repeat with remaining batter (or use a second muffin tin if you have it.)