Mycotoxins are secondary metabolites produced by certain fungi, posing significant health risks to humans and animals through contaminated food and feed. These fungi, and consequently the mycotoxins which they produce, are strongly influenced by weather, and this shifts over time due to climate change, leading to more frequent and severe events, such as heat waves, storms, and heavy rainfall. This study investigates how long-term weather trends and climatic factors impacted mycotoxin levels in corn samples over a 17-year period (2006–2022) across 12 countries, with a focus on 136 specific weather features. Among all potential relationships, we found Aspergillus toxins and fumonisins to be positively correlated with temperature, while deoxynivalenol and zearalenone are negatively correlated. Additionally, the dew point, particularly its 90th percentile value, is positively correlated with Aspergillus mycotoxins. We also identified significant patterns associated with wind direction. Collectively, these findings offer a comprehensive overview of mycotoxin–weather correlations, which may also be projected into future scenarios.