Understanding what causes weather-related stresses that lead to crop failures is a critical step towards stabilizing global food production. While there are many sources of weather-related stresses, the 30-60 day Madden-Julian Oscillation (MJO) is the dominant source of subseasonal climate variability in the tropics, making it a potential – but as of yet unexplored – source of crop failures. Here crop models and observational yield statistics are used to assess whether the MJO affects maize yields. We find that the influence of the MJO is widespread, affecting crop yields throughout the tropics. In dry, hot environments the MJO can lead to crop failures by reducing precipitation, decreasing soil moisture, and increasing extreme heat, while in wetter, cooler environments - where water stress is less common - MJO-forced decreases in rainfall bring increases in solar radiation that benefits crop yields. These results provide a pathway to develop actionable early warnings using subseasonal forecasts.