Nanoparticles are used in a variety of products, including fertilizer-nutrients and agro-pesticides. However, due to heightened reactivity of nano-scale materials, the effects of nanoparticle nutrients on crops can be more dramatic when compared to non nano-scale nutrients. This study evaluated the effect of nano manganese-(Mn) on wheat yield and nutrient acquisition, relative to bulk and ionic-Mn. Wheat was exposed to the Mn types in soil (6 mg/kg/plant), and nano-Mn was repeated in foliar application. Plant growth, grain yield, nutrient acquisition, and residual soil nutrients were assessed. When compared to the control, all Mn types significantly (p < 0.05) reduced shoot N by 9–18%. However, nano-Mn in soil exhibited other subtle effects on nutrient acquisition that were different from ionic or bulk-Mn, including reductions in shoot Mn (25%), P (33%), and K (7%) contents, and increase (30%) in soil residual nitrate-N. Despite lowering shoot Mn, nano-Mn resulted in a higher grain Mn translocation efficiency (22%), as compared to salt-Mn (20%), bulk-Mn (21%), and control (16%). When compared to soil, foliar exposure to nano-Mn exhibited significant differences: greater shoot (37%) and grain (12%) Mn contents; less (40%) soil nitrate-N; and, more soil (17%) and shoot (43%) P. These findings indicate that exposure to nano-scale Mn in soil could affect plants in subtle ways, differing from bulk or ionic-Mn, suggesting caution in its use in agriculture. Applying nano Mn as a foliar treatment could enable greater control on plant responses.