We propose a joint tracking architecture for multiple frequency signals originated from the same GNSS satellite in order to improve the reliability of position solution by making use of redundancy of multiple frequency signals. A joint higher order tracking loop is used to track the signal dynamics common across multiple frequency signals and a narrow individual signal tracking loop is used to track an uncommon residual carrier phase variation due to frequency dependent error sources. A suitable collaboration across multi-frequency signal tracking improves the individual signal tracking sensitivity and the robustness to frequency selective interference. Furthermore, joint signal tracking improves the receiver resistance to intentional interference such as jamming and spoofing. Performance of the proposed architecture is verified with live multi-frequency satellite signals collected from GPS Block-IIF satellites under the influence of frequency selective matched spectrum jamming signal.