Abstract Fugitive methane leakage from legacy oil and gas wells is assessed using surface flux and soil‐gas measurements, yet these signals are modulated by meteorology and shallow processes, obscuring sustained leakage. Whether persistent leakage leaves a coherent imprint in the shallow subsurface remains unresolved. Here we present a multi‐year field investigation at a decommissioned gas well, integrating repeated CH4–CO2 efflux surveys with geophysical and geochemical measurements. Surface flux mapping reveals a compact emission core despite strong interannual variability. In contrast, electromagnetic conductivity and geochemistry record broader, co‐centered responses extending meters beyond the flux core. These observations define a nested, multi‐scale geophysical–geochemical footprint anchored to a common source. The contrasting scales reflect temporal integration, with flux capturing instantaneous emissions and subsurface properties preserving longer‐term alteration. Our results show that sustained methane leakage reorganizes shallow conditions, providing a transferable framework for delineating leakage at legacy wells and informing monitoring of subsurface energy systems.