Post-harvest fungal diseases of plant products are a serious concern leading to economic losses and health risks. Moreover, the use of synthetic chemical fungicides to prevent these diseases is limited due to toxic residues. This study aimed at determining the effective dose of extracts of Trichoderma asperellum IMI393899 (TE1) and Trichoderma atroviride TS (TE2) in inhibiting the contamination by mycotoxigenic fungi on different plant matrices. Extracts were tested on tomatoes contaminated by Fusarium verticillioides and Fusarium graminearum, wheat contaminated by Penicillium verrucosum and maize contaminated by Aspergillus flavus. The efficacy of extracts was evaluated at two time intervals after treatment, 4 and 11 days for tomato, and 10 and 20 days for both wheat and maize. Both extracts showed a significant inhibitory activity on mycotoxigenic pathogens and significantly reduced Log CFU/g compared to the control. Moreover, the extracts reduced mycotoxin production in a dose dependent manner and with a long-lasting effect. The ochratoxin A was reduced by both extracts but only the extract TE2 was effective in reducing aflatoxins, whereas TE1 treatment increased their synthesis.