Whisk the flours, sugar, baking powder, baking soda, salt, and poppy seeds together in a large bowl.
In a second large bowl, whisk together the Greek yogurt, milk, butter, eggs, lemon juice, zest, and vanilla extract until well combined.
Pour the wet ingredients into the bowl with the dry ingredients and gently mix until just combined, making sure there are no dry patches of flour in the bottom of the bowl. Do not overmix.
Heat a skillet or griddle over medium-low heat and spray with cooking spray.
Pour about ⅓ cup of batter into the skillet and cook for 2-3 or until bubbles appear on the surface.
Flip and cook for 2 minutes on the other side, or until fully cooked and golden brown on both sides. Spray the skillet with cooking spray before cooking the next pancake.