The deep roots of volcanic systems play a key role in the priming, initiation, and duration of eruptions. Causative links between initial magmatic unrest at depth and eruption triggering remain poorly constrained. The 2021 CE eruption at Fagradalsfjall in southwestern Iceland, the first deep-sourced eruption on a spreading-ridge system monitored with modern instrumentation, presents an ideal opportunity for comparing geophysical and petrological data sets to explore processes of deep magma mobilization. We used diffusion chronometry to show that deep magmatic unrest in the roots of volcanic systems can precede apparent geophysical eruption precursors by years, suggesting that early phases of magma accumulation and reorganization can occur in the absence of significant increases in shallow seismicity (<7 km depth) or rapid geodetic changes. Closer correlation between geophysical and diffusion age records in the months and days prior to eruption signals the transition from a state of priming to full-scale mobilization in which magma begins to traverse the crust. Our findings provide new insights into the dynamics of near-Moho magma storage and mobilization. Monitoring approaches optimized to detect early phases of magmatic unrest in the lower crust, such as identification and location of deep seismicity, could improve our response to future eruptive crises.