Carbonatites and associated alkaline silicate rocks are of considerable economic interest due to their enrichments in rare earth elements. The petrogenesis and source(s) of these complexes, however, are poorly understood. Models propose either mantle plume-derived carbon-rich melts or a mantle source enriched by subduction-related metasomatism. We use zircon trace elements to fingerprint carbonatite-alkaline complex sources, focusing on the economically significant 1.4 Ga Mountain Pass intrusive suite (MPIS). Autocrystic zircon from MPIS alkaline silicate rocks are enriched in Th and U relative to Nb suggesting a subduction influenced, oxidized source region. Lower Sc/Yb, higher Ti concentrations, and the absence of Eu anomalies in autocrystic zircon suggest derivation from a less hydrous, hotter, and deeper mantle source relative to arc-related 1.8–1.6 Ga inherited zircon. These data are best explained by syn- to post-collisional Mesoproterozoic reactivation of a subduction-metasomatized mantle source. The source and tectonic setting of the MPIS contrasts with Mesoproterozoic Gifford Creek and Bayan Obo carbonatites which exhibit plume-like compositions and are associated with rifts, suggesting different sources and tectonic settings for these economically significant deposits. We demonstrate that zircon petrochronology is a robust method for distinguishing carbonatite sources and can inform more targeted exploration strategies for critical mineral resources.