Preheat your oven to 400°F and grease a standard 12-cup muffin tin with butter or cooking spray, making sure to coat the bottom and sides of each cup thoroughly. While the oven heats, zest your lemons to get the 3 tablespoons of freshly minced zest—I always zest before juicing to avoid losing any precious oils—and juice the lemons to get 1/4 cup of juice. Set both aside. Allow your eggs and butter to come to room temperature (about 70°F) if they aren't already, as this helps create a more emulsified, tender batter.

In a medium bowl, whisk together the flour, baking powder, baking soda, and salt. I like to sift the salt with the dry ingredients to remove any lumps and ensure even distribution of leavening agents throughout the batter. Set this dry mixture aside—don't over-mix, just combine until there are no visible streaks of unmixed flour.

In a large bowl, whisk together the Greek yogurt, room-temperature eggs, and sugar until well combined and slightly pale, about 1-2 minutes. Add the cooled melted butter, milk, lemon juice and zest from Step 1, vanilla extract, and almond extract, whisking until the mixture is smooth and homogeneous. The yogurt and lemon juice will create a tangy, moist crumb, so make sure everything is fully incorporated. This wet base should look creamy and uniform before you combine it with the dry ingredients.

Pour the wet mixture from Step 3 into the bowl with the dry ingredient mixture from Step 2. Add the poppy seeds to the wet mixture before folding everything together. Using a rubber spatula or wooden spoon, gently fold the ingredients together until just combined—do not overmix, as this can develop too much gluten and create tough, dense muffins. Stop folding as soon as you don't see any visible streaks of dry flour; a few small lumps are perfectly fine and actually desirable for tender muffins. The batter should be thick but pourable.

Divide the batter from Step 4 evenly among the 12 greased muffin cups, filling each about two-thirds to three-quarters full. Use a standard ice cream scoop or spoon to keep portions consistent, which ensures even baking. Place the muffin tin in the preheated 400°F oven and bake for 17-22 minutes, until the tops are golden brown and a toothpick inserted into the center of a muffin comes out clean or with just a few moist crumbs. The muffins should spring back when lightly touched on top.

Remove the muffin tin from the oven and let the muffins cool in the pan for 10 minutes—this resting period allows the crumb structure to set and makes them easier to remove without breaking. After 10 minutes, gently turn the muffins out onto a wire cooling rack and let them cool completely. This prevents the bottoms from becoming soggy from condensation if left in the warm pan too long.