The advent of genome editing techniques, together with advances in plant genomics, has made it possible to introduce precise modifications into key genes involved in plant responses to biotic and abiotic stress and quality traits, overcoming the limitations of both classical mutagenesis and the transgenic paradigm. Using genome editing, we have generated new ideotypes of potato resistant to infection by a major viral pathogen, as well as tomato plants characterized by extended shelf life, fortified with anti-inflammatory and anti-obesity molecules, tolerant to drought stress, more prone to establish symbiotic relationship with fungi, and containing reduced levels of allergenic or anti-nutritional compounds.