Preheat the oven to 400 degrees. Coat a muffin tin with cooking spray.
Combine the flours, baking powder, baking soda, and salt together in a dish.
Combine the yogurt, sugar, egg, milk, oil, vanilla, and lemon zest together in a bowl. Mix until well combined. Slowly add the flour mixture to the yogurt mixture until just combined. Add most of the cherries and blueberries to the batter, gently mix. Scoop spoonfuls of batter equally into each muffin tin. Side Note: I made a batch of 10 large muffins instead of 12 smaller ones. Gently push a few more cherries and blueberries into the top of each muffin.
Place into the oven and bake for 15-17 minutes or until a tester inserted into the center comes out clean. Let them cool for 5 minutes before placing them on a rack to continue cooling. Enjoy!