Heat oven to 350 degrees F. Line a 12-cup muffin pan with paper baking cups; spray lightly with cooking spray and set aside.

Whisk together milk and apple cider vinegar in a measuring cup or bowl; set aside.

In a large bowl or bowl of a stand mixer, whisk together flours, flaxseed meal, baking soda, cinnamon and salt. In a separate large bowl, whisk together maple syrup, vegetable oil and vanilla; add milk mixture and stir to combine.

Make a well in the center of the dry ingredients; add the wet ingredients and stir until just combined. Fold in cranberries, cherries and granola.

Divide batter evenly among muffin cups. Bake until golden brown and a toothpick inserted in the center comes out clean, about 20 minutes. Remove from oven; cool muffins in muffin pan for 5 minutes. Remove from pan and cool completely on a cooling rack.