Nanosized elemental sulfur (ES) is already reported to exert superior antimicrobial efficacy than micron-sized ES, which encourages their use in drugs and therapeutics. The aim of the present study is to explore the possible route and mode of antimicrobial action of orthorhombic (alpha-SNPs) and monoclinic (beta-SNPs) allotropes of sulfur, respectively, at their nano-dimensions. The antimicrobial efficacy of alpha-and beta-SNPs was determined against both the conventionally ES-resistant and ES-susceptible fungi and bacteria. Both the SNPs inhibited the microbial growth, irrespective of their resistance profile to ES and caused significant deformities on the microbial cell surfaces. However, the extent of antimicrobial efficacy was found to be optimum for a-SNPs, which can be attributed to their size, shape, and surface modification. Subsequent transcript profiling, metabolite profiling, and enzymatic analyses revealed that alpha- and beta-SNPs impaired a cluster of mitochondrial enzymes involved in cellular respiration and oxidative phosphorylation. ES and SNPs stress were found to elicit the NADPH-dependent glutathione reductase mediated ES-detoxification response in fungi and caused them to undertake the glyoxylate shunt in favor of energy conservation. A simultaneous study was also undertaken to assess the bio-compatible or bio-adverse properties of SNPs in terms of their cytotoxic and genotoxic effects against the human derived lung fibroblast cell line (MRC-5). The present study hence explores the antimicrobial physiology of two novel functional materials and demonstrates their compatibility as a future putative antimicrobial drug.