Preheat your oven to 350°F. Line baking sheets with parchment paper.
In a medium bowl, whisk together the flour, baking soda, and salt.
In a large bowl, beat the softened butter, granulated sugar, and brown sugar until creamy.
Add the eggs one at a time, mixing well after each addition. Stir in the vanilla extract.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined.
Stir in 1 cup of M&Ms.
Place rounded 2-tablespoon scoops of dough onto the prepared baking sheets, leaving about 2 inches between each.
Bake for 9 to 11 minutes, or until the edges are lightly golden. Use the remaining 1/4 cup of M&Ms to press into the top of the cookies.
Let the cookies cool on the baking sheet for 2 minutes, then transfer to a wire rack to cool completely.