The disclosed computer-implemented method for improving quality of service within hybrid storage systems may include (1) monitoring a performance measurement of a hybrid storage system that includes first and second types of storage devices that handle I/O throughput in connection with an application, (2) determining, based at least in part on the monitored performance measurement, an approximate amount of the I/O throughput handled by the first type of storage device over a period of time, (3) determining, based at least in part on the approximate amount of I/O throughput, a rate at which the application is allowed to deliver subsequent I/O throughput to the hybrid storage system over a subsequent period of time, and then (4) regulating, based at least in part on the rate, the subsequent I/O throughput in connection with the application over the subsequent period of time. Various other methods, systems, and computer-readable media are also disclosed.