The development of environmentally friendly alternatives to plant protection products is essential for sustainable agriculture. In this context, natural compounds, such as enzymes, proteins, and peptides, represent a promising reservoir of bioactive molecules. Although little represented on the market, their potential as fertilizers, biostimulants, and biopesticides is highlighted by numerous reports and patents, which the present review aims to bring together. While fertilization and biostimulation are primarily aimed at improving plant yield and health, biopesticides can be used to target a wide range of microbial plant pathogens and pests. The nature and effects of proteinaceous molecules are discussed in light of restrictive regulations.