A sensitive and reliable multi-mycotoxin method was developed for the simultaneous determination of 16 mycotoxins in dried fruits using liquid chromatography (LC) combined with electrospray ionization-triple quadrupole tandem-mass spectrometry. Mycotoxins have been extracted from the samples using a modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) procedure. In an effort to enforce the knowledge on mycotoxin occurrence and co-occurrence in dates and dried fruits, 228 samples purchased from Tunisian and Spanish markets were subjected to multi-mycotoxin liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis of 16 mycotoxins. At least one mycotoxin was detected in 160 samples (70%). The frequency of contaminated samples was 83%, 80%, 64%, 59% and 26% for dates, dried vine fruits, figs, apricots and plums, respectively but none of the analysed samples contained detectable levels of fumonisins (FB1, FB2 and FB3) or T-2 toxin (T2). The incidence and levels of mycotoxins varied in samples. The most prevalent mycotoxin was Enniatin B (EnnB) (54%), followed by Enniatin A1 (EnnA1) (36%); aflatoxins (AFs) (23%) and ochratoxin A (OTA) (22%). Thirteen samples contained AFs in levels that exceed the maximum limits established in EU legislation. The simultaneous contamination with 2 to 6 mycotoxins was observed in 51% of the analyzed samples. Lastly, intakes of the detected mycotoxins were calculated for average adult consumers and compared with the tolerable daily intakes (TDI). Data obtained were used to estimate the potential exposure levels. Isothiocyanates (ITCs) are natural compounds produced by enzymatic conversion of metabolites called glucosinolates. They are potentially useful antimicrobial compounds for food applications. In this study, the reduction of the FBs present in loaf bread contaminated with Gibberella moniliformis CECT 2987, a fumonisin producer by allyl (AITC), phenyl (PITC) and benzyl isothiocyanates (BITC) was investigated. In addition, the antifungal activity of these ITCs towards Fusarium mycotoxigenic strains was also evaluated. The ITCs employed in this study inhibited the growth of three mycotoxigenic Fusarium, reducing 2.1 to 89.7% of the mycelium size. The ITCs used also reacted with the FB2 produced by G. moniliformis in the bread, reducing its levels by 73 to 100 % depending on the dose and time of exposure. Then, gaseous ITC was used to fumigate corn kernels and corn flour contaminated with FBs produced by Gibberella moniliformis CECT 2987 in situ. Mycotoxin levels were evaluated using liquid chromatography coupled to mass spectrometry in tandem (LC-MS/MS), while products formed from the reaction of FBs and ITCs were examined by liquid chromatography coupled to mass spectrometry-linear ion trap (LC-MS-LIT). The reduction of FB1 and FB2 in solution ranged from 42 to 100% on a time-dependent manner. This variance was greatly influenced by pH. In general, lower pH levels eased the reaction between ITCs and FBs. ITC fumigation treatment (50, 100 and 500 µL/L) was able to reduce 53 to 96% of FB1 levels, 29 to 91% of FB2 and 29 to 96% of FB3. Four reaction products between the bioactive compounds employed in this study were identified, corresponding to FB + ITC conjugates.