Place two racks in the upper and lower thirds of the oven and preheat to 350°F. Line two baking sheets with parchment.
In a large bowl, whisk together the flour, baking powder, baking soda and salt.
In another large bowl, cream the butter and sugar with a handheld mixer or stand mixer just until the butter and sugars are blended, about 2 minutes. Use a spatula to scrape down the sides of the bowl. Add the eggs one at a time, mixing until each is combined. Mix in the vanilla.
Add the flour mixture to the bowl and blend on low speed until the flour is barely combined, about 30 seconds. Scrape down the sides and bottom of the bowl.
Add the chocolate all at once to the batter. Mix on low speed until the chocolate is evenly combined. Use a spatula to scrape down the sides and bottom of the bowl and if needed stir and knead the batter to incorporate all of the ingredients.
Scoop mounds of dough about 1-2 tablespoons in size onto the baking sheets, leaving 3 inches between them.
Bake the cookies for 16-18 minutes until set.
Place the baking sheet on a rack for a few minutes, then transfer the cookies to the rack to cool fully. Repeat with the remaining dough. Cookies are best eaten warm from the oven or later that same day. They'll keep in an airtight container for up to 3 days.
Notes
Use room temperature ingredients. Bring the butter and eggs to room temperature for a bit before you add them to the dough. Or, heat the butter in the microwave for 10 seconds. In gluten-free baking, the butter and sugar must be properly aerated for the best results, so I try not to use butter that's too cool.
Do a double batch of dough: To save some cookie dough for later, double the ingredient amounts and freeze half of the dough. Thaw the dough in the fridge then bake it according to the recipe directions.
Bake as bars: To make these into chocolate chip cookie bars similar to my super deliciously buttery gluten-free chocolate chip bars, press the dough into a buttered and parchment-lined 9x13 pan and bake for 30-35 minutes.
Make dairy-free: Use non-dairy butter in place of the of the butter.
Make refined sugar-free: Substitute coconut sugar for the brown sugar and granulated sugar.
Other flour - You can do an equal combo of whole wheat flour and all-purpose flour if you wish, or use spelt flour or whole wheat pastry flour instead of whole wheat flour.
Make gluten-free - Make these cookies with gluten-free oat flour to make them gluten-free! Simply substitute 420 grams of oat flour for the whole wheat flour.
Flaky salt - Top cookies with flaky sea salt for the perfect sweet-salty touch.
Make ice cream sandwiches - These whole wheat chocolate cookies are PERFECT for making ice cream cookie sandwiches. Fill them with a big scoop of vanilla, chocolate, or caramel ice cream for a treat.