The emerging risk management metrics, FSO, PO and PC, were applied to the aflatoxins (AFs) and ochratoxin A (OTA) determination in 8 commercial lots of pistachio. In order to determine the sampling uncertainty, two sampling plans (EU official sampling and company plan) in quadruplicate, and two analytical methods (ELISA and HPLC), were considered in parallel. The combination of EU official sampling plan and HPLC proved to be the most appropriate option. The major variability was associated with the subfraction selection and, therefore, increasing the number of the analysed subfractions could be an alternative for reducing uncertainty. AFs were present in all lots, mainly AFB1 and AFB2, while OTA was never detected. The effect of toasting on AFs presence in pistachio (a performance criteria, PC) was evaluated in order to achieve a given PO, taking into account the FSO, i.e., the EC limits. Percentages of AFs reduction were 87.62% ± 11.89, 81.05% ± 15.51 and 86.74% ± 11.31 for AFB1, AFB2 and total AFs, respectively. Given an initial AFB1 and AFBs level ≤12 μg/kg and ≤15 μg/kg, respectively, the toasting would ensure the AFB1 and AFs legal limits compliance before human consumption (FSO).