Metschnikowia pulcherrima includes strains of applied agro-food interest, particularly due to the antimicrobial activity against plant pathogens, contribution to the aroma of fermented beverages, and preliminary evidence related to probiotic activity. This biotechnological relevance sheds new light of interest on the biology of this yeast. To better understand and expand its biotechnological potential and applicability, the genomes of M. pulcherrima NRRL Y-7111( T), NRRL Y-48695, CBS 10357, and NRRL Y-48712 were sequenced, and de-novo assembled. Between 10,671 and 14,548 genes were predicted and the cooperative genomic analyses were integrated with experimental assessments relating to traits relevant for biotechnological application and safety. In silico and in vitro safety assessment revealed intermediate sensitivity for itraconazole; furthermore, variants of the genes related to pulcherrimin production and transport were found in all the genomes. Moreover, an arsenal of carbohydrate-active enzymes (CAZymes) was unravelled, and their predicted localization was investigated. This study expands the body of knowledge on M. pulcherrima, including traits relevant for defining its safety as a bioresource, which is a pivotal aspect for its possible inclusion in the European Food Safety Authority (EFSA) Qualified Presumption of Safety (QPS) list and its application in REgulated food/feed PROducts (REPRO) both in the European Union & aligned European countries. KEY POINTS: • A pipeline for genomic characterisation and safety assessment of unconventional yeasts, using M. pulcherrima as a model species was developed. • M. pulcherrima strains can be considered safe and safety data can be used to develop a body of knowledge to include M. pulcherrima in EFSA QPS list. • Analysis of the predicted localization of CAZymes allowed the detection of compounds as potential biological control agents.