One of the most prevalent and practical uses of nanotechnology is encapsulating active chemicals in mesoporous silica SBA-15 to improve their functional performance. Encapsulation techniques can be used to increase the potency of essential oils (EOs), making them more commercially viable. The general objective of this work was to encapsulate peppermint (Mentha aquatica L.) essential oils in mesoporous silica SBA-15 and to assess their antifungal efficacy against the phytopathogens Botrytis cinerea and Colletotrichum nymphaeae. The EOs extracted from the leaves of peppermint very effectively inhibited C. nymphaeae and B. cinerea mycelium at 5, 10 and 15 days after incubation. Encapsulating the M. aquatica L. EOs increased the inhibition of mycelium growth of C. nymphaeae by 16.8, 32.5, and 66.3% after 5, 10, and 15 days of incubation, respectively. Meanwhile, mesoporous silica-encapsulated EOs decreased mycelium growth by 35.20, 8.12, 10.40, and 8.15% at concentrations of 100, 1000, 1500, and 2000 ppm. Our work reveals that when nano-encapsulated EOs are administered, significant morphological changes occur in the fungal mycelium. D-limonene (4.904%), menthone (30.18%), p-menthone (7.03%), and menthol (52.11%) were identified as the primary components in M. piperita EOs using GC-MS analysis. In conclusion, the encapsulation of peppermint EO with SBA-15 was demonstrated to be efficient in controlling B. cinerea and C. nymphaeae growth and can be comparably applied as eco-friendly and safe antifungal agents to the management of plant diseases.