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The majority of soil carbon resides in mineral-associated organic matter (MAOM) in most soils. MAOM is assumed to be relatively inert to environmental change because it is protected from microbial activity thus contributing substantially to soil carbon storage. However, plants and associated microbes may destabilize MAOM through mineral dissolution and exchange reactions in the rhizosphere, potentially causing soil carbon loss. Here, we quantified the magnitude of MAOM destabilization in the rhizosphere in response to extreme precipitation dynamics expected with climate change. To do this, we followed the fate of labeled MAOM (13C microbial necromass adsorbed to iron minerals: goethite or ferrihydrite) in the wheat (Triticum aestivum L.) rhizosphere during a 12-week pot experiment subjected to precipitation regimes mimicking the status quo (optimal conditions) as well as extreme intermittent droughts and flooding as is expected in central Europe with climate change. We found that MAOM destabilization was significantly greater under flooding compared to optimal and drought conditions. MAOM destabilization was particularly accentuated in MAOM initially bound to poorly crystalline ferrihydrite compared to MAOM initially bound to more crystalline goethite. Our results suggest that MAOM bound to poorly crystalline minerals (ferrihydrite) may be particularly vulnerable to destabilization in the rhizosphere during intense precipitation events, contributing to soil carbon loss. With the increasingly extreme nature of precipitation events, understanding the underlying MAOM destabilization mechanisms in the rhizosphere is essential for better predictions of the soil carbon response to environmental change.