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Explaining mutualistic cooperation between species remains one of the greatest problems for evolutionary biology^,,,. Why do symbionts provide costly services to a host, indirectly benefiting competitors sharing the same individual host? Host monitoring of symbiont performance and the imposition of sanctions on ‘cheats’ could stabilize mutualism^,. Here we show that soybeans penalize rhizobia that fail to fix N₂ inside their root nodules. We prevented a normally mutualistic rhizobium strain from cooperating (fixing N₂) by replacing air with an N₂-free atmosphere (Ar:O₂). A series of experiments at three spatial scales (whole plants, half root systems and individual nodules) demonstrated that forcing non-cooperation (analogous to cheating) decreased the reproductive success of rhizobia by about 50%. Non-invasive monitoring implicated decreased O₂ supply as a possible mechanism for sanctions against cheating …