BB's and Caffe Nero will also participate in the voluntary scheme which finds each coffee and sandwich shop pledging individual initiatives to improve the nutritional value of their food and drink. They will be reviewed by the FSA every six months.
Most notably will be new calorie labelling on all of Pret A Manger's products, which have been criticised in the past for their heavy mayonnaise content, some sandwiches tipping the scales at 500 or more calories.
Pret has also pledged to reduce the level of salt in their soups and increase the number of half-size "slim Pret" sandwiches.
Starbucks, BB's, Nero and Costa -- where often a coffee and muffin can account for nearly half of an adult's daily calorie allowance -- have all pledged to review their product range to see where healthier changes can be made.
Starbucks will also display the calorie count of its food and aims to reduce the sodium and fat levels from its 10 most popular products by September of this year.
Greggs has pledged to remove all hydrogenated fats and artificial colours and flavours from its pies by June 2010.
Eat will lower sodium content across its entire product range and will post the calorie content of its food online.
It is estimated that coffee-shop takeaway meals account for a quarter of the food eaten by UK residents.
The campaign comes on the heels of a recent government study that said 60% of men, 50% of women and 25% of children in the UK will be obese by 2050.
The move follows initiatives taken by many of the country's fast food restaurants, including McDonald's, KFC, Burger King and Subway, who pledged to improve their menus under a similar campaign with the FSA.