When it comes to raising the level of quality of your ingredients, it ultimately increases the cost of those ingredients as well. And while many QSRs and fast-casual restaurants do their best to not pass those costs along to customers, it can be difficult to strike a balance between quality and increasing cost of doing business at a higher level.
At a minimum, restaurants that choose higher-quality ingredients (fresh produce, animals raised without antibiotics, etc) can expect a two percent increase in their food costs.
Associated with this cost is something that many people don't often think about - the cost of food safety training for the proper handling of higher quality (and fresher) foods. The cost of this kind of training can be high - and with a generally high turnover rate in the QSR-fast casual industry, brands are looking at a lot of money spent on food - and training on how to properly handle that food.