New plate reconstructions constrain the tectonic evolution of the subducting Cocos and Nazca plates across the southern Central American subduction zone from late Miocene to recent. Because of the strong relationships between lower and upper (Caribbean) plate dynamics along this margin, these constraints have wide‐ranging implications for the timing and growth of upper plate deformation and volcanism in southern Central America. The reconstructions outline three important events in the Neogene history of this margin: (1) the coeval development of the Panama Triple Junction with the initiation of oblique subduction of the Nazca plate at ∼8.5 Ma; (2) the initiation of seamount and rough crust subduction beginning at ∼3–4 Ma; and (3) Cocos Ridge subduction from ∼2 to 3 Ma. A comparison of these events with independent geologic, geomorphic, volcanic, and stratigraphic data sets reveals that the timing, rates, and origin of subducting crust directly impacted the Neogene growth of upper plate deformation and volcanism in southern Central America. These analyses constrain the timing, geometry, and causes of a number of significant tectonic and volcanic processes, including rapid Plio‐Quaternary arc‐fore arc contraction due to Cocos Ridge subduction, the detachment of the Panama microplate at ∼1–3 Ma, and the late Miocene cessation of mantle‐wedge‐derived volcanism across ∼300 km of the subduction zone.