The present disclosure provides systems and methods for manufacturing shelf-stable, multi-compartment products. In a general embodiment, a manufacturing system is provided and includes a continuous manufacturing line including a barrier separating a dry food packaging area from a wet food packaging area. The manufacturing line is configured to manufacture a shelf-stable food product including both a dry food product with no artificial preservatives in a first compartment of a tray and a wet food component with no artificial preservatives in a second compartment of the tray.