Preheat the oven to 375 degrees. Lightly grease a 12-cup standard muffin tin or line with paper liners. If using liners, lightly greasing them as well. Set aside.
In a medium bowl, whisk together the whole wheat pastry flour, baking powder, baking soda, and salt. In a large mixing bowl, beat together the peanut butter, brown sugar, and coconut oil until well combined. Beat in the eggs 1 at a time, fully incorporating and scraping down the bowl between each. Beat in the vanilla.
With the mixer on low speed, gently add 1/3 of the flour mixture. Once it has disappeared, add 1/2 of the buttermilk (pour it slowly so that it doesn't splatter), the next 1/3 of the flour, the remaining buttermilk, then the remaining flour. Fully incorporate between each addition and mix the batter just until everything is combined—do not over beat. Stir in the chocolate chips.
Scoop the batter into the prepared muffin pan. Bake until the tops are golden brown and a toothpick inserted in the center comes out clean, 18 to 22 minutes. Remove from the oven and let cool in the pan for 5 minutes, then gently turn the muffins out onto a cooling rack to cool completely.
Leftover muffins can be stored in an airtight container at room temperature for 3 days or individually wrapped and frozen for 1 month.