Add the butter, peanut butter, granulated sugar, and brown sugar to the bowl of a stand mixer fitted with the paddle attachment. Beat on high speed for 3 minutes, until light and fluffy.
Meanwhile, combine the flour, baking soda, salt, baking powder, and nutmeg in a separate bowl, whisking to combine. Set aside.
Scrape down the bowl of the stand mixer. Beat in the eggs and egg yolk, one at a time, beating well after each addition. Scrape down the bowl and beat in the vanilla.
With the mixer running on low speed, gradually beat in the dry ingredients until only a few streaks of flour remain. Scrape down the bowl and remove the bowl from the mixer.
Add the chocolate chips and candies to the cookie dough, mixing by hand with a wooden spoon or rubber spatula. Make sure you mix in any dry dough that may be left at the bottom of the bowl, this always happens to me!
Cover the bowl and chill the cookie dough for at least 1 hour, but up to 3 days. When you're ready to bake your cookies, preheat the oven to 350°F. Roll the dough into balls and place them evenly spaced apart on a sheet pan lined with parchment paper. Alternatively, you can freeze the dough balls and bake them only when you want to eat them.
If you want, press some extra candies and chocolate chips onto the outsides of the dough balls before you bake them, that way they'll be more visible when they're done! The candy eyeballs should be added after baking.
Bake the cookies for 11 to 13 minutes - just until the edges begin to turn golden brown. If they still look underbaked in the centers, that's ok. They will continue to cook on the sheet pan when you remove it from the oven.
Press a few candy eyeballs onto the baked cookies, and sprinkle them with flaky sea salt, if desired.
These cookies are more fragile, so let them cool down enough for you to pick them up without any breaking. Serve warm or store in an airtight container for 3 to 5 days.
Notes
Scroll up to read about any ingredient substitutions and baking tips!