Nowadays, one of the major problems in agriculture remains the struggle against pathogens, especially fungi. In the last 60 years, the use of large amounts of pesticides to increase crop yield caused environmental pollution, loss of biodiversity, and the development of multi-resistant plant pathogens. Now, more than ever, agriculture practises must become environmentally friendly and thus, new strategies to improve agriculture, without side effects for the environment and human health, need to be developed. Antimicrobial photodynamic treatment (APDT) has emerged as an alternative treatment that can be envisaged in agronomic practices to fight against microorganisms, without harming plants. To develop this approach on complex living systems such as grapevine and potato, hosts of the fungus pathogen Botrytis cinerea and two photosensitizers were taken into consideration: an anionic porphyrin (TPPS) and a natural chlorin Chlorophyllin (Chl). More specifically, an extensive work was conducted using photoactivated TPPS. TPPS was very effectively inhibit Botrytis cinerea development and it did not cause any phenotypical or biochemical alterations of the grapevine varieties (Merlot, Chardonnay and Sauvignon). In the potato varieties, while there were alterations in its growth and development, the plants were able to defend themselves. Furthermore, in order to find a new eco-friendly solution that is more suitable for a large range of plants we tested a natural PS: the chlorophyllin (Chl). Surprisingly, Chl was able to inhibit Botrytis cinerea mycelium growth without disturbing neither potato nor grapevine plantlet growth. In conclusion, these preliminary studies based on the use of Chl suggest that the development of a safe but efficient APDT approach in agriculture may no longer be a dream