Preheat the oven to 350 F. In a medium bowl, whisk together flour, salt, and baking soda. In a large bowl, mix together butter, peanut butter and both sugars until fluffy.
Add in the flour mixture, and mix until it is fully combined. Fold in the M&Ms. Press the cookie dough into a greased 8-inch square baking dish and bake for 20-25 minutes.