Preheat the oven to 350-degrees F. Line two large baking sheets with parchment paper and set aside.
In the bowl of an electric mixer fitted with a paddle attachment, cream together the peanut butter, butter and sugars. Beat in the eggs. Add in the baking soda, wheat germ and milled flax seed and vanilla extract. Mix to combine.
Add in the quick cooking oats, chocolate chips and M&M candies and mix well.
Drop by rounded tablespoonfuls onto the prepared baking sheet.
Cook for 10-12 minutes until golden brown, taking care not to over bake.
Let set 2 minutes before transferring to a wire rack to cool. Store cookies in an airtight container or bag for up to 1 week.