Combine the whole wheat pastry flour, oat flour, sugar, baking powder, baking soda, and salt to a large mixing bowl and whisk together.
Pour the milk, yogurt, oil, and vanilla in a separate small bowl and whisk until completely combined. Pour liquid mixture into the dry mix and stir with a fork until just mixed and no more flour is seen. Stir in chocolate chips.
Heat a cast-iron skillet or non stick griddle over medium heat. Place a small amount of butter on the pan and coat the cooking surface. Drop ¼ cupfuls of batter 2 inches apart onto the skillet.
Cook until the edges are set and air bubbles form on top, about 2-3 minutes. Flip and cook 1-2 minutes more until the underside is golden.