Soil contamination with metals and metalloids is a growing environmental concern, impacting soil ecosystems. Exogenous metal(loid)s are retained in the soil matrix via adsorption, structural incorporation, and precipitation, imposing stress on soil microbiomes, potentially influenced by climate. It remains unclear whether introduced metal(loid)s bind similarly to native ones and how quickly soil microbiomes adapt under today’s and future climate conditions. We incubated soils spiked with 0.7 mg kg⁻¹ cadmium or 15 mg kg⁻¹ arsenic under today’s and future climate scenarios (IPCC SSP 3–7.0: +400 ppm_v CO₂, +4°C). After 38 days, spiked As and Cd did not integrate into soil minerals like native counterparts but preferentially associated with more reactive minerals. Spiked As became more recalcitrant over time, an effect enhanced under future conditions. Spiked Cd remained reactive during incubation, independent of climate conditions. Prokaryotic abundances increased faster in metal(loid)-spiked soil under future conditions with distinct soil prokaryotic community structures emerging in response to metal(loid)s and climate. Despite this, key functions like Fe(III) reduction were maintained. Communities nearly stabilized within 38 days across climate conditions. These findings suggest that exogenous metal(loid)s may require years to achieve native-level binding, while soil microbes adapt functionally within weeks, even under climate change.