The lower crust plays a critical role in the processing of mantle melts and the triggering of volcanic eruptions by supply of magma from greater depth. Our understanding of the deeper parts of magmatic systems is obscured by overprinting of deep signals by shallow processes. We provide a direct estimate of magma residence time in basaltic systems of the deep crust by studying ultramafic nodules from the Borgarhraun eruption in Iceland. Modeling of chromium-aluminum interdiffusion in spinel crystals provides a record of long-term magmatic storage on the order of 1000 years. This places firm constraints on the total crustal residence time of mantle-derived magmas and has important implications for modeling the growth and evolution of transcrustal magmatic systems.