Chromium (Cr) stress negatively impacts plant growth and physiological processes, making it a significant environmental concern. This study investigates the effectiveness of selenium nanoparticles (Se-NPs) in mitigating Cr stress on plants, comparing its efficacy with traditional selenium (Se). Nevertheless, research on using soil-applied Se-NP to lessen Cr buildup in plants has not been widely documented as of now. Here, we investigate the effectiveness of Se-NPs in mitigating Cr stress on plants, comparing their efficacy with traditional Se and control. Under the pervasive influence of Cr stress, Se-NPs exhibit remarkable superiority over conventional Se, significantly enhancing growth parameters (fresh weight, dry weight, shoot length, and root length), respectively, compared to the Cr-stressed plants. Physiologically, Se-NPs outperform Se by substantially improving the net photosynthesis rate (+32%), transpiration (+147%), and stomatal conductance (+64%), indicating its exceptional contribution to fortifying plant resilience under Cr stress. In mitigating oxidative stress, Se-NPs surpass Se, demonstrating a more pronounced reduction in LOX activity (−35%), MDA levels (−34%), H2O2 (−37%), and MG (−47%), showcasing heightened protection against Cr induced oxidative damage. Antioxidant defense systems also witness greater activation under Se-NPs, with higher increases in SOD (+27%), CAT (+54%), GPX (+7%), and GST (+37%) activities. Moreover, under Cr stress Se-NPs induce a more profound upregulation of antioxidant genes and the production of secondary metabolites, emphasizing its superior impact on the plant's defense mechanisms. The modulation of the ASA-GSH cycle by Se-NPs is more robust, with increased levels of ASA (+69%) and GSH (+33%), and decreased DHA (−28%) and GSSG (−29%), suggesting a more effective antioxidant network. Moreover, Se-NPs demonstrate heightened interference in Cr uptake in both root (−30%) and shoot tissues (−23%), indicating its potential to disrupt the Cr-induced ASA-GSH cycle. The study highlights the potential of Se-NPs as a more effective and sustainable approach to mitigate Cr-induced stress in plants, emphasizing the importance of understanding the underlying mechanisms and optimizing application strategies for improved agricultural sustainability and productivity in Cr-contaminated environments. Furthermore, it is necessary to conduct economic feasibility studies and assessments of the effects of Se-NP on soil microbiota in order to promote the widespread application in agricultural activities.