01 - Preheat the oven to 375°F. Line a 12-cup muffin tin with paper liners or grease each cup lightly.
02 - In a medium bowl, whisk together the all-purpose flour, baking powder, baking soda, and salt until evenly distributed.
03 - In a large bowl, whisk the melted butter, honey, Greek yogurt, eggs, lemon zest, orange zest, lemon juice, orange juice, and vanilla extract until smooth and well combined.
04 - Pour the dry ingredients into the wet mixture and gently fold together until just combined. Be careful not to overmix to keep the muffins tender.
05 - Divide the batter evenly among the prepared muffin cups, filling each about three-quarters full.
06 - In a small bowl, combine the flour, granulated sugar, thyme leaves, and sea salt. Add the cold cubed butter and rub it in with your fingers or a pastry cutter until the mixture resembles coarse crumbs.
07 - Sprinkle the thyme crumble generously over each filled muffin cup, pressing lightly 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 tin for 5 minutes, then transfer them to a wire rack to cool completely before serving.