Preheat oven to 350 degrees. Whisk together flour, baking powder, baking soda and salt in a large bowl, set aside.
With a mixer, beat lemon zest and agave nectar on medium speed. Add butter. Cream with agave and lemon zest until light and fluffy, another 2-3 minutes. Mix in the lemon juice. Add flour mixture; mix until just combined and no flour pockets remain. Chill for about 45 minutes.
Roll rounded teaspoons of dough in 3/4-in balls; place 2 inches apart onto parchment lined baking sheets. Sprinkle with poppy seeds. Bake 10-12 minutes, rotating after 5 minutes until edges are just set.