Nano-engineered delivery systems have emerged as possible solutions for more efficient pest management in agriculture. Likewise for nanostructured drug delivery systems (DDS) in medicine, the use of biocide delivery systems (BDS) brought concerns on their toxicology on non-targeted organisms. Plants, for instance, are the foundation of the ecosystem, acting as primary actor in the food chain and is associated with the whole biodiversity, being strictly related to human health. This is a very important consideration to fully understand the benefits of using delivery systems for crop protection and production. Herein, a biocide delivery system was prepared by loading nanostructured, microscaled, biogenic silica particles with thymol, a known phytotoxicant. The resulting system contains 120 mg of thymol per gram of silica and displays slow release features. The Allium cepa bioassay was chosen to demonstrate how the toxicity and cellular damages induced by thymol can be significantly reduced through a slow, controlled, release strategy. The lower mobility of the reference particles associated with slow-delivery features reduced the toxicity and cellular damages caused by thymol in the plant genetic model.