Manganese (Mn) deficiency is prevalent in rice-growing regions resulting in poor paddy yield and human health. In this study, role of Mn, applied through various methods, in improving the productivity and grain biofortification of fine grain aromatic rice was evaluated. Manganese was delivered as soil application (SA) (0.5 kg ha−1), foliar spray (FA) (0.02 M Mn), seed priming (SP) (0.1 M Mn) and seed coating (SC) (2 g Mn kg−1 seed) in conventional (puddled transplanted flooded rice) and conservation (direct seeded aerobic rice) production systems at two different sites (Faisalabad, Sheikhupura) in Punjab, Pakistan. Manganese application, through either method, improved the grain yield and grain Mn contents of fine grain aromatic rice grown in both production systems at both sites. However, Mn application as SC and FA was the most beneficial and cost effective in improving the productivity and grain biofortification in this regard. Overall, order of improvement in grain yield was SC (3.85 t ha−1) > FA (3.72 t ha−1) > SP (3.61 t ha−1) > SA (3.36 t ha−1). Maximum net benefits and benefit–cost ratio were obtained through Mn SC in flooded field at Faisalabad, which was followed by Mn SP in direct seeded aerobic rice at the same site. However, maximum marginal rate of return was noted with Mn SC in direct seeded aerobic rice at both sites. In crux, Mn nutrition improved the productivity and grain biofortification of fine grain aromatic rice grown in both conventional and conservation production systems. However, Mn application as seed treatment (SC or SP) was the most cost effective and economical.