A fungus Sphaerodes mycoparasitica SMCD 2220-01 is a host specific mycoparasite against plant pathogenic Fusarium species. Fusarium spp. are producing a plethora of mycotoxins including zearalenone (ZEN), deoxynivalenol (DON) and its acetylated derivatives, 3-acetyl-deoxynivalenol (3-ADON) and 15-acetyl-deoxynivalenol (15-ADON). The SMCD 2220-01 strain substantially reduced DON, 3-ADON, 15-ADON, and ZEN production capacity in co-culture system. Degradation and detoxification of the pure mycotoxins were also achieved when exposed to SMCD 2220-01 in shake flasks. The thin layer chromatography (TLC) combined with high performance liquid chromatography–electrospray ionization-high resolution mass spectrometry (HPLC–ESI–HRMS) revealed that the amount of mycotoxins exposed to SMCD 2220-01 was considerably reduced compared to control. ZEN level was decreased by 97%, while zearalenone sulfate ([M−H+SO3]− at m/z 397.1052 C18H21O8S1) was detected as a metabolite of ZEN converted to less toxic molecule by the mycoparasite. Further, the mycoparasite appeared to degrade DON, 3-ADON, and 15-ADON by 89, 58, and 72%, respectively. The deoxynivalenol sulfate ([M−COCH3+SO3−CH2O]− at m/z 345.2300 C14H17O8S1) was detected as a less toxic metabolic product of DON and 3-ADON. These findings report the SMCD 2220-01 effectiveness to lower mycotoxins-producing capacities of Fusarium, degrade pure mycotoxins and transform them to less toxic metabolites, opening new opportunities for research and innovation for detoxification of mycotoxins.