In this study, a field experiment was conducted to evaluate the growth and yield responses of Sri Lankan lowland rice (Oryza sativa L.) with the application of beneficial Arbuscular mycorrhizal fungi (AMF) inoculum, and inter-cropping with highly mycorrhizal dependent vetiver grass (Chrysopogon zizanioides L.) under two different soil nutrient management systems (NMSs): conventional/chemical (CNMS) and organic (ONMS). The experiment was designed as a split plot with three blocks. Each CNMS and ONMS experiment included untreated control (T0), and three treatments—AMF inoculation (T1), vetiver intercropping (T2), and the combination of AMF and vetiver (T3). According to the results, colonization of rice roots with AMF was not affected significantly by the treatments and ranged from 0‒15.8%. The effect was very low or absent in the early stage and then higher in the later stages of the rice plant. Furthermore, plant growth was not significantly different between the two NMSs, although grain yield was significantly higher (P < 0.05), with the order T1 (0.45 kg/m2) >T2 (0.42 kg/m2) >T3 (0.41 kg/m2) in CNMS and T2 (0.44 kg/m2) >T1 (0.41 kg/m2) >T3 (0.40 kg/m2), in ONMS than for the respective controls (T0), thus suggesting beneficial utilization of AMF and vetiver in the lowland rice farming system.