Preheat your oven to 400°F / 200°C.
Grease a 12-cup standard muffin tin with butter or line with paper liners.
In a large bowl, whisk together the whole wheat flour, cornmeal, rye flour, baking powder, baking soda, and salt. Make a well in the center of the dry .
In a separate medium bowl, beat the buttermilk, egg, vegetable oil, and honey together until smooth and well combined.
Pour the wet into the well of the dry .
Stir with a spatula just until the flour is moistened.
Do not overmix; a few lumps in the batter are perfectly fine.
Divide the batter evenly among the 12 prepared muffin cups, filling each about two-thirds full.
Bake for 18-20 minutes, or until the tops are golden brown and a toothpick inserted into the center of a muffin comes out clean.
Let the muffins cool in the tin for 5 minutes before transferring them to a wire rack to cool slightly.
Serve warm for the best experience.
Let the batter rest on the counter for 10-15 minutes before baking. This allows the flours to fully hydrate, resulting in a more tender crumb and a better rise.
Using room temperature buttermilk and egg will help the batter come together more easily and create a more uniform, evenly baked muffin.