Essential oils that have antifungal activity and mycotoxin reduction ability are candidates to develop bioactive alternatives and environmentally friendly treatment against phytopathogenic fungi. However, their practical use is affected by their high volatility, UV sensitivity, and fast oxidation. Encapsulation techniques are supposed to provide protection to the essential oils and control their release into the environment. Ammoides pusilla essential oil proved to be an efficient inhibitor of Fusarium avenaceum growth and its production of mycotoxins, enniatins. In the present work, A. pusilla essential oil was encapsulated, using the impregnation method, into mesoporous silica particles with narrow slit pores (average diameter = 3.1 nm). The particles were characterized and their activities against the fungi were evaluated in vitro. Encapsulation of the essential oil into mesoporous silica particles improved significantly its stability and its antifungal and antimycotoxin properties. It is a promising tool for the formulation of a natural fungicide that could be used in the agriculture or food industry to protect plant or food products from the contamination by toxigenic fungi such as Fusarium sp. and their potential mycotoxins.