Display omitted •Fertilisation combined with AMF affected the composition and quality of tomato fruits.•AMF increased nitrogen, manganese, and hydrophilic phenol content in tomato fruits.•Interaction between fertilisation and AMF application modified tomato fruit volatiles.•The effect of AMF inoculation might depend on native AMF and environmental conditions. The effects of different fertilisation treatments with arbuscular mycorrhizal fungi (AMF) inoculation on AMF root colonisation, fruit yield, nutrient and total phenol contents, volatile compound composition, and sensory attributes of tomato (Solanum lycopersicum L.) were investigated. Mineral, organic, and mineral + organic fertiliser application positively affected tomato yield (35%–50%) and phosphorus concentration (24%–29%) compared with controls. AMF application had a significant impact on the total nitrogen (+9%), manganese (+12%), and hydrophilic phenol (+8%) contents in the fruit. Volatile compounds were affected by the interactive effects of fertilisation and AMF application. The response of tomato fruit sensory quality indicators was relatively modest, with only a few sensory characteristics affected to a lesser extent. Although tomato showed susceptibility to field-native AMF, particular combinations of fertilisation and AMF inoculation were more effective at improving the quality parameters of tomatoes under field conditions applied in this study.