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Abstract The northern Sierra Nevada batholith was emplaced into and across a series of accreted crustal belts that vary considerably in their ages and lithologies. Unlike batholithic segments to the south, the northern Sierra comprises smaller, spatially distinct plutons where geologic relations with the host basement can be observed. Intermediate to felsic plutons were sampled as arc‐perpendicular transects at the latitude of Lake Tahoe and zircon Lu‐Hf and trace element analysis was performed in order to assess the relative impacts of temporal and spatial variability of arc magmatism on zircon geochemistry. Trends through time in the Hf data are complex, whereas there is an abrupt step from juvenile values in plutons intruding western belts (+12.3 to +14.4) to more evolved values in those intruding the Northern Sierra terrane to the east (−0.6 to +5.2). A similar pattern is observed in several zircon trace element signatures, including pronounced steps toward higher U/Yb, Dy/Yb and Ce/Y from the western belts into the Northern Sierra terrane to the east. The step is approximately coincident with the Feather River terrane, which is interpreted to mark the suture between the oceanic lithosphere to the west and the North American continental lithosphere to the east. The observed links between variation in zircon Lu‐Hf and trace element concentration and basement domain indicate that northern Sierran zircons incorporate, and are sensitive to, the crustal tracts into which they are emplaced. Preliminary application of our results to provenance analysis of Great Valley strata indicates changing provenance through time in the adjacent forearc.