A tonneau cover storage system for a vehicle includes a cargo compartment having a first sidewall and a cargo opening. A cavity is formed in the first sidewall. A container is pivotably attached to the first sidewall proximate the cavity at a first pivot point, and has a container opening sized and shaped to selectably fit into the cavity. A lid to selectably close off the container opening is also pivotably attached to the first pivot point and is pivotable independently of the container. A flexible tonneau cover is selectably configurable between a stowed condition within the container and a deployed condition closing off the cargo opening. The container is movable to a position within the cavity when the tonneau cover is in the stowed condition, and is further movable to a position outside the cavity when the tonneau cover is in the deployed condition.