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Preheat your oven to 375℉ and line a 12-hole muffin tin. Set aside.
In your blender, combine cooked and peeled beets, eggs, oil, maple syrup, yogurt, and vanilla. Blend until beets are totally pureed. Set aside.
In a large bowl, mix together flour, cocoa powder, baking soda, baking powder, and salt until combined.
Pour contents of blender into the bowl with dry ingredients. Stir together with a spoon or spatula until just combined, being careful not to over mix. Over mixing can lead to dense muffins, so mixing until just combined is important for achieving fluffy muffins. Fold in chocolate chips.
Divide batter evenly between the prepared muffin tin compartments and top with additional chocolate chips, if desired.
Bake in preheated oven for 18 minutes or until a toothpick inserted into the middle comes out clean. TIP: If you have a kitchen thermometer, bake until your muffins are 200℉ in the center. This will ensure they are cooked through but aren't over baked, which can result in a dry muffin.
Let cool 10 minutes before transferring the muffins to a wire cooling rack and/or enjoying. Allow leftovers to cool completely before storing in an air-tight container in your fridge for 4-5 days or in your freezer for up to a month.