One of the biggest challenges facing humanity is the need to maintain adequate food supplies in the face of growing world population. To achieve this, we need to have effective tools protecting crops against a variety of parasites that can cause crop losses. While pesticides are the traditional means of addressing this problem, with time they become less effective due to parasite adaptation, and also we become more conscious of their potential negative impact on the environment, as well as on human health. One very promising technology that can provide an effective and safe approach to protecting plants against parasites is RNA interference, also known as “gene silencing”. This work has used mathematical models to establish strategies for optimal use of nutrients and pesticides that improve plant growth and protect plants against parasites, while also minimising pesticide use. Mathematical models of RNA interference have helped understand main features of this process, and this was then used for the development of natural microbial biostimulants that, besides improving crop performance, provide a targeted protection against specific parasites, while avoiding detrimental effects on the environment.