Mix water, yeast, and honey together in the bowl of a stand mixer fitted with a dough hook; let sit until yeast is dissolved, about 5 minutes.
Combine bread flour, whole wheat flour, flax seed meal, and salt in a bowl. Add flour mixture and olive oil to yeast mixture. Mix on low speed for 5 minutes. Increase speed to high and knead for 5 minutes more. Cover bowl with plastic wrap and let sit in a warm place until dough doubles in size, about 1 hour.
Transfer dough to an oiled work surface about the same size as the pizza pan. Flatten dough with oiled hands by pressing it in the middle and working to the edges until dough has been flattened to the size of pizza pan.
Oil the pizza pan and invert it over the dough. Pick up the work surface and the pizza pan and invert the whole stack so the dough ends up on the pizza pan. If the dough doesn't come off right away, just set it down and the dough should fall onto the pizza pan within 5 minutes. Pull the edges of the dough to the edge of the pizza pan; let rest for 10 minutes.