Mycotoxins are secondary metabolites of filamentous fungi that contaminate food products such as fruits, vegetables, cereals, beverages, and other agricultural commodities. Their occurrence in the food chain, especially in beverages, can pose a serious risk to human health, due to their toxicity, even at low concentrations. Mycotoxins, such as aflatoxins (AFs), ochratoxin A (OTA), patulin (PAT), fumonisins (FBs), trichothecenes (TCs), zearalenone (ZEN), and the alternaria toxins including alternariol, altenuene, and alternariol methyl ether have largely been identified in fruits and their derived products, such as beverages and drinks. The presence of mycotoxins in beverages is of high concern in some cases due to their levels being higher than the limits set by regulations. This review aims to summarize the toxicity of the major mycotoxins that occur in beverages, the methods available for their detection and quantification, and the strategies for their control. In addition, some novel techniques for controlling mycotoxins in the postharvest stage are highlighted.