Preheat oven to 350 degree F. Line 12 regular size muffin holes with paper liners.
Place the beets into the large basket and start steamer cycle for 20 minutes. Let cool slightly and then puree. Measure out 1/2 cup of the puree for this recipe and reserve the rest for another batch of muffins or another recipe. Beet puree can be frozen for 3 months.
In a medium bowl, whisk together the flour, sugar (if using maple syrup blend with wet ingredients), cocoa powder, baking powder, salt, cinnamon and cloves.
In the blender you used to puree the beets (no need to wash), blend together the milk, oil, beet puree and vanilla extract for 45-60 seconds. Add in the egg and pulse for 10 seconds.
Add the wet ingredients into the dry ingredients and stir until just combined.
In a small bowl, add the cream cheese and maple syrup and microwave for 20 seconds. Whisk until smooth.
Fill each muffin hole with 1 heaping tablespoon of muffin mix, make a slight indent in the muffin mix with the back of your spoon. Spoon 1 teaspoon of cream cheese filling into each indented hole. Cover with another heaping tablespoon of muffin mix, making sure to cover the cream cheese completely.
Bake in oven for 18-20 minutes or until a toothpick comes out clean. Let cool and serve.