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This paper will describe the various challenges experienced and their resolving techniques during RF characterization of spacecraft onboard antennas in Compact Antenna Test Facility (CATF) of ISRO Satellite centre (ISAC), Bangalore. ISAC-CATF has rich experience of successfully testing 8 spacecrafts covering wide frequency range from L-band to Ka-band with Linear and circular polarization. Effect of spacecraft body and its mounting location on low-gain, wide beam Telemetry and Telecommond Antenna and criticality in measuring cross-pol component of payload antenna is discussed. Challenges experienced in RF characterization of onboard Ka-band Tracking antenna and special requirement of zero-g are also discussed. ISRO's experience in transponder characterization of multiple spot beam antenna is shared and spacecraft level PIM measurement in presence of metallic range reflectors is presented.