Abstract During the last decades, food security has become a vital global concern driven by projections of population increase and exacerbated by the impending pressure of climate change on agriculture. Vegetable crops represent a fundamental ingredient of human diet due to their high nutritional value and bioactive content and could serve towards improving food security and nutritional quality, especially when managed under highly intensified cropping systems in controlled environments. Greenhouse and indoor growing modules not only allow for significantly higher yields compared to open field cropping systems, but also they can facilitate out of season production and substantial manipulation of the chemical composition and bioactive profile of the final product. The present work provides an updated critical overview of scientific advances regarding genotype and microclimate effects on the quality of greenhouse crops. In this context, innovative crop management practices are discussed, including management of the nutrient solution, biofortification and application of plant biostimulants. The review concludes by proposing future research pathways towards enhancing product quality of greenhouse vegetables.