In a medium bowl, whisk together the flour, baking soda, baking powder, and salt. Whisking first helps distribute the leavening evenly through the flour. Set this bowl aside while you work on the wet ingredients so everything is ready to combine quickly.
Beat the softened butter and sugar together for a full two to three minutes until it turns pale and fluffy. This step is where a lot of the cookie's chewy texture comes from, so don't rush it. Scrape down the bowl halfway through for an even mix.
Mix in the egg and vanilla extract until fully combined and smooth. The batter should look glossy and slightly thickened at this stage. This is also when the dough starts smelling like a proper bakery.
Add the flour mixture in two batches, mixing on low speed just until combined. Overmixing here can make your cookies tough instead of soft, so stop as soon as the flour disappears. The dough will look thick and slightly sticky, which is exactly right.
Split the dough into three equal portions and knead a different gel food color into each one, purple, orange, and green. Wearing food-safe gloves keeps your hands from turning into a monster's hands too. You can keep the colors separate or twist them together for a marbled look.
Wrap each colored portion and refrigerate for at least 30 minutes. Chilling firms up the butter so the cookies hold their shape and bake up thicker instead of spreading thin. This is an easy step to skip, but I really don't recommend it.
Once chilled, scoop the dough into balls and gently press a few mini M&M's into the top of each one. Doing this before baking lets the candy sink in slightly as the cookie spreads. Space the dough balls about two inches apart on your lined baking sheet.
Bake at 350°F for 9 to 11 minutes, just until the edges look set but the centers still appear soft. The cookies will continue cooking slightly on the hot pan after you pull them out. This carryover baking is what keeps the centers so wonderfully chewy.
While the cookies are still warm, press candy eyeballs onto each one so they stick into the soft surface. Waiting too long makes the eyes fall right off once the cookie firms up. Let the cookies cool completely on a wire rack before serving or storing.