Recently, hand sanitization has gained attention for preventing disease transmission. Many on-the-market convenient dermal sanitizers contain alcohol, which can be detrimental to the skin. Therefore, three nanoemulgel formulations (LN-F1, LN-F2, LN-F3) incorporating lemon peel extract (LE), and with various increasing concentrations of xanthan gum as a gelling agent and stabilizer, were developed and characterized as a novel alternative. All formulations showed non-Newtonian shear-thinning flow behavior, particle size values below 200 nm, and increasing zeta potential with higher xanthan gum concentrations. All nanoemulgel formulations exhibited greater in vitro phenolic compound release than free LE. LN-F2 (1.0% LE, 20.0% mineral oil, 20.0% Span 80, 4.0% Cremophor RH 40, 4.0% PEG 400, 0.5% xanthan gum, 50.5% dH2O) was selected as the optimal formulation due to improved characteristics. LE and LN-F2 potential cytotoxicity was assessed on MA-104, showing no significant cellular morphological alterations up to 10 mg/mL for both samples. LN-F2 showed in vitro antimicrobial activity against E. coli, S. Typhimurium, P. aeruginosa, S. aureus, L. monocytogenes, and C. albicans, as well as antiviral activity against phiX 174, but no effect against rotavirus (SA-11). In vivo, LN-F2 presented a removal capacity of 83% to 100% for bacteria and 89% to 100% for fungi. These findings suggest that the formulated nanoemulgel holds potential as a safe and effective antiseptic, providing a viable alternative to commercial alcohol-based formulations.