Precision genome-editing techniques, in particular CRISPR-Cas9, have revolutionised the management of agricultural diseases by allowing targeted modifications of resistance (R) genes, susceptibility (S) genes and targets of pathogen agents. This transformative approach provides unprecedented control of the interaction between plants and pathogens, enabling the development of crops with increased resistance to a variety of biotic stresses, including bacterial, viral and fungal pathogens. Recent advances have demonstrated the ability of CRISPR-Cas9 to precisely modify key genetic components, while integrating with multi-omics (transcriptomics, proteomics and metabolomics) technologies to identify new mechanisms of resistance and optimise the editing strategy. This development makes it easier to produce new, more stable crops under the pressure of climate change and to tackle critical food security challenges. However, the wide deployment of CRISPR-edited crops faces several obstacles, including regulatory uncertainty, potential unintended effects and public acceptance issues, which need careful consideration. Despite these challenges, CRISPR-Cas9 is a powerful tool for sustainable agriculture, offering precise manipulation of plant immunity and stress response, which contributes to building a more resilient and sustainable global food system. Continued innovation in genome editing, combined with responsible management and public involvement, will be crucial for realizing its full potential in meeting the complex challenges of modern farming.