The Franciscan Complex of California, the type example of an exhumed accretionary complex, records a protracted history of voluminous subduction accretion along the western margin of North America. Recent geochronological work has improved our knowledge of the timing of accretion, but the details of the accretionary history are disputed, in part, due to uncertainties in regional-scale correlations of different units. We present new detrital zircon U-Pb ages from two sites on opposite sides of San Francisco Bay in central California that confirm previously proposed correlations. Both sites are characterized by a structurally higher blueschist-facies unit (Angel Island unit) underlain by a prehnite-pumpellyite-facies unit (Alcatraz unit). The Angel Island unit yields maximum depositional ages (MDAs) ranging from 112 ± 1 Ma to 114 ± 1 Ma (±2σ), and the Alcatraz unit yields MDAs between 94 ± 2 Ma and 99 ± 1 Ma. Restoration of post-subduction dextral displacement suggests these sites were originally 44–78 km apart and much closer to other Franciscan units that are now exposed farther south in the Diablo Range. Comparison with detrital zircon dates from the Diablo Range supports correlations of the Bay Area units with certain units in the Diablo Range. In contrast, correlations with Franciscan units in the northern Coast Ranges of California are not robust: some units are clearly older than those in the Bay Area whereas others exhibit distinct differences in provenance. Integration of age data from throughout the Franciscan Complex indicates long-lived and episodic accretion from the Early Cretaceous to Paleogene. Although minor, sporadic accretion began earlier, significant accretion occurred during the interval 123–80 Ma and was followed by minor accretion at ca. 53–49 Ma. Periods of accretion and non-accretion were associated with arc magmatism in the Sierra Nevada–Klamath region, cessation of arc activity, and reorganization of paleodrainage systems, which implicates plate dynamics and sediment availability as major controls on the development of the Franciscan Complex.