Numerous bioadditives can be applied in protected cultivation of vegetables for enhancement of their growth, yield, increase of tolerance to environmental stresses (including drought, nutrient deficiency and others) and, in particular, improving food quality of a crop. Several bioadditives' applications have been tested in three greenhouse experiments including microbial inoculation with arbuscular mycorrhizal fungi (AMF), Trichoderma harzianum and plant growth-promoting bacteria (PGPB). In addition, the effects of amendments with slow-release organic-matter-based fertilizer, an organic matter preinoculated with saprophytic fungi (SF), a solution with an algal mixture or a synthetic phytohormone-derived analogue were tested in combination with microbial treatments. Bioadditives were tested on tomato and pepper in pot experiments using horticultural substrates. Some positive responses to particular combinations of bioadditives as regards growth and/or yield were observed. In addition, parameters of increased contents of health promoting compounds were reported in some applications on tomato: content of total antioxidant capacity and vitamin C. We suggest that the use of AMF compatible with selected strains of biocontrol fungus T. harzianum or AMF in combination with SF treated organic matter or organic matter-based fertilizer can be successfully used in production of tomatoes and other vegetable crops in particular in protected horticultural cultivation in soilless substrates. The use of bioadditives in commercial vegetable production offers an ecological way of cultivation while possibly improving food quality and health promoting properties of vegetable crops based on increased accumulation of health-promoting phytochemicals. Bioadditives can be an integral beneficial part of ecological, organic vegetable production.