01 - Preheat the oven to 350°F. Line a 12-cup muffin tin with paper liners or grease the cups generously.
02 - In a large bowl, whisk together the all-purpose flour, baking powder, baking soda, and salt until evenly distributed.
03 - In a separate bowl, combine the honey, granulated sugar, lemon zest, orange zest, whole milk, fresh orange juice, fresh lemon juice, melted butter, and eggs. Whisk until smooth and well blended.
04 - Pour the wet mixture into the dry ingredients and gently fold with a spatula until just combined. Be careful not to overmix—a few lumps are perfectly fine.
05 - Divide the batter evenly among the prepared muffin cups, filling each about three-quarters full.
06 - In a small bowl, mix the flour, light brown sugar, fresh thyme leaves, and a pinch of salt. Add the cold cubed butter and rub with your fingertips until the mixture resembles coarse crumbs.
07 - Sprinkle the thyme crumble evenly over each filled muffin cup, pressing gently so it adheres to the batter.
08 - Bake for 20 to 22 minutes, or until a toothpick inserted into the center of a muffin comes out clean and the tops are golden.
09 - Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely before serving.