There are many ways to apply Six Sigma to food manufacturing. As a matter of fact, there are many food manufacturers that apply Lean and/or Six Sigma tools to improve the process, especially fast food industries that manufacturer and deliver food.
With perishable product and large quantities of food being produced and/or delivered, often the goals are around Quality and Speed! Quality can be defined in many ways, but ultimately, reducing variation in the food product in taste and portion size consistency. For SPEED: insuring that fresh, quality food is delivered where it is needed and when it is needed in the best condition possible. There could be opportunities to identify and attack waste.
An example of waste, in this case, could be moving food product unnecessarily causing delays in delivery to customers. Another example is making too much food and having to discard excess inventory.
I hope that helps!