Disclosed herein is a system including analog receive paths and analog transmit paths and signal processing equipment onboard a satellite, and methods for use therewith. For each of a plurality of the analog receive paths, a calibration signal is injected therein below a noise floor thereof, while the path is actively used to receive and condition an RF signal, and the calibration signal is extracted from the analog receive path after the signal has traveled through at least a portion of the path. The extracted calibration signal is compared to the injected calibration signal to determine gain and phase deviations caused by the path. Gain and phase characteristics of the analog receive paths are adjusted to compensate for different gain and phase deviations being caused by different paths. Similar techniques are used to compensate for different gain and phase deviations being caused by different analog transmit paths.