This work tackles the quest for temperature-responsive greener solvents by synthesizing a hydrophobic deep eutectic solvent (DES) comprising menthol and decanoic acid. The low solubility of hydrophobic solvents in polar media was addressed by dispersing DES as oil-in-water nanoemulsions allowing their use in biomedical applications. DES-in-water nanoemulsions produced by ultrasound and membrane emulsification techniques were systematically compared. Microengineered isoporous membranes having 9 μm pore size were fabricated by laser machining. A membrane pitch of 100 μm was optimized to produce nanoemulsions 58.7 ± 0.4 nm in size at a dispersed phase flow rate of 0.02 mL min −1 leading to a new approach termed as membrane-assisted nanoemulsification. Subsequently, the optimized DES-based nanoemulsions subjected to antimicrobial susceptibility testing assays were 32 times more active against the Gram-positive bacteria, S. aureus ATCC 6538, than against the Gram-negative bacteria, E. coli ATCC 8739. In contrast to the nonemulsified DES or its individual components, 16 times less chemicals were required to inhibit bacterial activity when tested as nanoemulsions, suggesting increased bioavailability and a synergistic effect of all components in nanoemulsions potentiating their antibacterial activity. Lastly, membrane-assisted nanoemulsification offers sustainable production of nanoemulsions with a better control over size and dispersity along with lowered energy consumption when compared to ultrasound emulsification.