Nanoparticles (NPs) have emerged as one of the most innovative and promising application in agriculture. Since plants are recognized as essential component of all ecosystems, the effects of NPs on plants may pave a new insight to the ecosystems. Here, uptake and translocation of superparamagnetic iron oxide NPs (SPIONs), with various surface charges, on soybean has been probed; in addition, the effects of SPIONs on variations of chlorophyll, in hydroponic condition, together with their ability for reduction of iron deficiency chlorosis were explored. We find that SPIONs, which were entered and translocated in the soybean, increased chlorophyll levels, with no trace of toxicity. Furthermore, it was found that physicochemical characteristics of the SPIONs had a crucial role on the enhancement of chlorophyll content in subapical leaves of soybean. The equivalent ratio of chlorophyll a to b, in all treatments with conventional growth medium iron chelate and SPIONs (as iron source), indicated no significant difference on the photosynthesis efficiency. Finally, it was observed that the effect of SPIONs on the soybean chlorophyll content may have influence on both biochemical and enzymatic efficiency in different stages of the photosynthesis reactions.