Line two baking sheets with parchment paper.
Combine flour, baking soda, cocoa powder, cream of tartar, and salt in a bowl and whisk together.
In the bowl of a stand mixer, or a large bowl with a hand-held electric mixer, beat butter on medium speed until smooth and creamy. Add peanut butter, sugar, and brown sugar. Mixed until combined and fluffy. Add vanilla and eggs and mix well.
Add half the flour mixture and mix until incorporated. Repeat with the second half of the flour. Add the peanut butter filled chocolate chips.
Cover and place the cookie dough in the refrigerator for about half an hour. Preheat the oven to 350 degrees. Scoop the cookie dough into balls and place on the prepared baking sheets about 1 inch apart. Bake for 11-12 minutes. Let the cookies cool for 5-10 minutes and repeat this process with the rest of the cookie dough.
If you'd like, you can also add peanut butter morsels and drizzle the cookies with melted peanut butter morsels after they've cooled.