01 - Preheat the oven to 375°F (190°C). Line a standard 12-cup muffin tin with paper liners or grease each cup lightly with butter.
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 with a spatula until just combined. Avoid overmixing 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 with your fingers or cut in with a pastry cutter until the mixture resembles coarse crumbs with some pea-sized pieces remaining.
07 - Sprinkle the thyme crumble generously over each filled muffin cup, pressing gently so the topping adheres.
08 - Bake for 20 to 22 minutes, or until the tops are golden and a toothpick inserted into the center of a muffin comes out clean.
09 - Let the muffins rest in the tin for 5 minutes, then transfer them to a wire rack to cool completely.