Line a baking sheet with parchment paper and set aside.
Whisk the flour, baking soda, instant coffee granules and salt together in a bowl, and set aside.
In a large bowl, add room temperature butter, brown sugar, and granulated sugar and beat on medium for about 3 minutes. Make sure to scrape the sides of the bowl in between mixing to get all the ingredients incorporated. After 3 minutes of beating, butter and sugar will become fluffy and lighter in color.
Add the egg and vanilla extract, mix until incorporated.
Add in the dry ingredients, mix on low until the flour is just combined. It's ok if you still see traces of flour left, we'll fold those in with chocolate later on.
Fold in the M&Ms and chocolate chips with a spatula.
With a cookie scoop or a spoon, scoop the cookies on the parchment paper, no need to leave space between them for now. Cover with plastic wrap and refrigerate for 1 hour or overnight.
Preheat the oven to 350°F (177°C). Line two baking sheets with parchment paper. Place cookies on the baking sheet. Make sure to leave enough room between the cookies because they spread while baking. Bake in the preheated oven for 6 minutes, rotate the baking sheet and bake 4 more minutes (Total bake time: 10 minutes). The edges will be a lightly browned but the center should be soft.
Once you take the cookies out of the oven and they're still hot, press a few more M&Ms and chocolate chips on top (optional).
Let the cookies cool down on the baking sheet for 10 minutes.
You can keep these cookies in an air tight container, at room temperature for a week.