Preheat oven to 375 degrees F and grease a 12-cup muffin tin with nonstick spray (or parchment liners).
Add the flours, baking powder, baking soda, and salt to a medium bowl. Stir.
Stir in the yogurt, honey, butter, eggs, vanilla, and lemon zest. Gently stir in the blueberries. (The batter will be thick.)
Divide the batter among the prepared muffin tin, using about 1/4 cup batter in each cup.
Bake for 18-20 minutes, or until golden brown around the edges and a cake tester inserted into the center comes out cleanly.
Let cool in the pan for a minute or two, then run a paring knife around the edges. Transfer to a wire rack and let cool fully.