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Preheat oven to 350º. Line 18 muffin cups with papers.
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In medium bowl, stir together flour, sugar, cocoa, baking powder and salt. Set aside.
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Once beets have cooled, rub gently to remove outer skins. They should come off easily. Place beets in food processor bowl and blend until smooth.
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Add milk, oil and vanilla to food processor. Blend again until smooth. Add dry ingredient mixture in 3 or 4 increments, blending and scraping down sides of bowl between additions.
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Remove blade from food processor and stir in chocolate chips.
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Divide half of batter between muffin cups. Place a dollop of cheesecake filling in the center of each, then top with remaining batter.
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Bake until tops spring back when lightly touched, 18-20 minutes. Transfer to cooling rack and allow to cool completely before removing from tins.