Mycotoxins, produced as secondary metabolites by specific filamentous fungi under certain conditions, pose a significant health risk when they contaminate nuts and nut products. These toxic compounds, particularly aflatoxins and notably aflatoxin B1 (AFB1), are among the most dangerous mycotoxins in the human diet due to their carcinogenic and immunosuppressive effects. In response, international food safety authorities have set limits for mycotoxin levels in nuts to mitigate these risks. To detect these mycotoxins, various methods have been developed, with high-performance liquid chromatography (HPLC) and ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-QqQ-MS/MS) standing out for their efficiency and sensitivity. Our review paper seeks to offer a detailed analysis of the primary mycotoxins affecting nuts, their health implications, and their prevalence across the globe. It also examines the pretreatment processes for nut samples, the analytical approaches for mycotoxin identification in nuts, and the latest developments in the materials and solvents used for these analyses. It also identifies significant challenges in mycotoxin detection in nuts, including variability in detection methods and a lack of comprehensive data from some nut-producing regions, underscoring the need for further research in these areas. In addition, the strengths and drawbacks of analytical methods for identifying mycotoxins in nuts are well explained.