Scholars of judicial institutions view presidential appointments as a powerful means of establishing long-term interbranch influence in settings with high judicial independence. However, in contexts where incumbents control judicial careers, conventional expectations suggest that judicial agents will favor the current executive rather than the appointing party. This paper argues that political polarization can reshape these incentives, inducing partisan bias even in environments where traditional theories would not predict it. We examine this dynamic in Argentina’s federal corruption investigations, focusing on the Comodoro Py courthouse, the nation’s most prominent federal circuit, over the period from 2013 to 2023. We leverage the random assignment of cases to courts to compare how prosecutors appointed by different presidents investigate cases involving politicians from the two main political parties. Our findings reveal significant partisan bias, with agents shielding partisan allies and persecuting out-party members in their investigations. These effects are especially pronounced among more ideologically extreme prosecutors, highlighting the enduring impact of political polarization on judicial behavior and challenging existing theories of executive influence over the judiciary.