Porous silica nanocarriers have the potential to improve agricultural crop productivity. However, the impacts of nanoencapsulated pesticides on soil health and plant growth, and how they compare with conventional pesticides have not been systematically elucidated. In this study, we investigated how applying azoxystrobin encapsulated in porous hollow SiO₂ nanocarriers to agricultural soil impacted the soil microbial community and plant development, using Solanum lycopersicum grown in the laboratory in soil microcosms. The data show that plant growth was heavily inhibited by the non-encapsulated pesticide treatment compared to that with encapsulated pesticide yielding 3.85-fold less plant biomass, while the soil microbial community experienced few to no changes regardless of the treatment. There was a 2.7-fold higher azoxystrobin uptake per unit dry plant biomass after 10 days of exposure for the non-encapsulated pesticide treatment when compared to that of nanoencapsulated pesticide, but only 1.5-fold increase in total uptake. After 20 days of exposure, however, the total uptake and uptake per unit of dry biomass were 3-fold and 10-fold higher, respectively, for the nanopesticide treatment. The differences in uptake can be attributed to phytotoxicity caused by the high bioavailability of the non-encapsulated pesticide. The nanocarrier promoted slow release of the pesticide over days, which prevented phytotoxicity, and allowed healthy plant growth.