The potential use of cabbage isothiocyanates to control Alternaria rot in bell pepper was tested. Solid phase microextraction and gas chromatography–mass spectrometry found allyl, benzyl, 2-phenylethyl and phenyl isothiocyanates in a ratio of 1:3.5:5.3:9.6, respectively, in cabbage leaves. The same proportion was used to prepare an isothiocyanate mixture from reagent grade isothiocyanates (MCIT) to test the effect on Alternaria alternata growth in vitro. Application of 0.28 and 0.56 mg/ml of MITC, with or without packing in low density polyethylene bags (LDPE), were also tested on bell pepper fruit inoculated with A. alternata, using a commercial fungicide as positive control. A concentration of 0.03 mg/ml of MITC inhibited 100% Alternaria growth in vitro. A treatment with 0.56 mg/ml of MCIT with LDPE bags performed better than the commercial fungicide to control fungi rot on bell pepper with no adverse effects on fruit quality. MCIT combined with LDPE bag showed potential to control Alternaria rot on bell pepper.