Green manures (GM) as an alternative to inorganic fertilizer offer considerable potential as a source of plant nutrients and organic matter (OM). Hence, field experiments were carried out during 2015 and 2016 cropping seasons to compare impacts of GM and NPK (15:15:15) fertilizer on soil properties, growth, fruit yield, mineral, lycopene and vitamin C contents of tomato (Lycopersicon esculentum Mill). GMs were composed by green tender stems and leaves of pawpaw (Carica papaya L.), neem (Azadirachta indica A. Juss.), moringa (Moringa oleifera Lam.) or gliricidia (Gliricidia sepium (Jacq.) Kunth ex Walp.) and applied at 5 Mg ha−1, whereas NPK was applied at 300 kg ha−1 and there was a no fertilizer plot (control). Application of GMs reduced soil bulk density and increased soil OM, N, P, K, Ca, Mg, growth, number of fruits and fruit yield of tomato compared with the control. NPK fertilizer had no effect on soil bulk density and soil OM, but it increased soil fertility and tomato yield as compared with the control. When comparing treatments, the highest tomato yield and best cost:benefit ratio were obtained with gliricidia as GM. The GMs and NPK fertilizer increased mineral, lycopene and vitamin C contents in tomato fruits and the highest K, Ca, Fe, Zn, Cu, lycopene and vitamin C contents in tomato fruits were found with moringa as GM. Our results revealed that GM has potential to improve soil properties, tomato yield and quality, being an alternative for cropping management.