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BACKGROUND: Pistachio fruits suffer from postharvest decay, caused by Aspergillus flavus. This results in aflatoxin B1 (AFB1) accumulation in kernels, which is hazardous for human health due to its carcinogenic activity. In this study, the mechanism used by exogenous β‐aminobutyric acid (BABA) treatment for attenuating Aspergillus decay, minimizing aflatoxin B1 (AFB1) accumulation, and maintaining nutritional quality in fresh‐in‐hull pistachio kernels, infected by A. flavus during storage at 25 °C for 18 days, was investigated. RESULT: Results of an in vivo assay showed that the spore germination and germ tube elongation of A. flavus was repressed by BABA treatment at 7.5 mM. Aspergillus decay accompanied by AFB1 accumulation was also minimized in fresh‐in‐hull pistachio kernels treated with BABA at 7.5 mM and infected by A. flavus. Fresh‐in‐hull pistachio kernels, infected by A. flavus, treated with BABA at 7.5 mM, also exhibited higher phenol and flavonoid accumulation and 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) scavenging capacity accompanied by higher phenylalanine ammonia lyase (PAL) enzyme activity. CONCLUSION: Promoting phenylpropanoid pathway activity with higher PAL enzyme activity in fresh‐in‐hull pistachio kernels treated with BABA may not only reduce Aspergillus decay in kernels by cell wall fortification but also may be favorable for maintaining the kernels' nutritional quality through its effects on ROS scavenging capacity. As oxidative stress, represented by ROS accumulation, is responsible for A. flavus growth and AFB1 accumulation, higher phenol and flavonoid accumulation in fresh‐in‐hull pistachio kernels treated with BABA may be beneficial for attenuating Aspergillus decay and minimizing AFB1 accumulation. © 2019 Society of Chemical Industry [ABSTRACT FROM AUTHOR]