Preheat & Prep Pan: Set your oven to 350°F. Lightly grease a standard 12-cup muffin tin using nonstick spray.
Melt Butter: Cut the butter into chunks and place in a microwave-safe bowl. Microwave in 30-second intervals, stirring in between, until just melted. Set aside to cool. Alternatively, use a heatproof bowl set over simmering water.
Mix Dry Ingredients: In a large bowl, combine both flours, baking powder, baking soda, and salt. Whisk until evenly distributed.
Combine Wet Ingredients: Add the honey to the cooled melted butter, then whisk in the Greek yogurt, eggs, lemon zest, lemon juice, vanilla extract, and almond extract until smooth. If the butter firms up again, microwave in short bursts or warm over simmering water until liquefied.
Bring Batter Together: Create a well in the center of the dry ingredients and pour in the wet mixture. Gently stir just until no dry flour remains. Fold in the chia seeds. The batter will be quite thick.
Bake: Evenly divide the batter among the muffin cups (about ¾ full). Bake for 18 to 22 minutes until the tops are golden and spring back when lightly touched, or a toothpick inserted in the center comes out clean. Cool the muffins in the pan for 5 minutes, then carefully loosen with a knife and move to a wire rack to cool fully.
Prepare the Glaze: In a small bowl, whisk the powdered sugar and lemon juice until smooth. Adjust the consistency by adding more lemon juice for a thinner glaze or more sugar for a thicker one. Drizzle over cooled muffins.