To overcome the increased disease rate, utilization of the versatile broad spectrum antibiotic drugs in controlled drug-delivery systems has been a challenging and complex consignment. However, with the development of microemulsion (μE)-based formulations, drugs can be effectively encapsulated and transferred to the target source. Herein, two biocompatible oil-in-water (o/w) μE formulations comprising clove oil/Tween 20/ethylene glycol/water (formulation A) and clove oil/Tween 20/1-butanol/water (formulation B) were developed for encapsulating the gatifloxacin (GTF), a fourth-generation antibiotic. The pseudoternary phase diagrams were mapped at a constant surfactant/co-surfactant (1:1) ratio to bound the existence of a monophasic isotropic region for as-formulated μEs. Multiple complementary characterization techniques, namely, conductivity (σ), viscosity (η), and optical microscopy analyses, were used to study the gradual changes that occurred in the microstructure of the as-formulated μEs, indicating the presence of a percolation transformation to a bicontinuous permeate flow. GTF showed good solubility, 3.2 wt % at pH 6.2 and 4.0 wt % at pH 6.8, in optimum μE of formulation A and formulation B, respectively. Each loaded μE formulation showed long-term stability over 8 months of storage. Moreover, no observable aggregation of GTF was found, as revealed by scanning transmission electron microscopy and peak-to-peak correlation of IR analysis, indicating the stability of GTF inside the formulation. The average particle size of each μE, measured by dynamic light scattering, increased upon loading GTF, intending the accretion of drug in the interfacial layers of microdomains. Likewise, fluorescence probing sense an interfacial hydrophobic environment to GTF molecules in any of the examined formulations, which may be of significant interest for understanding the kinetics of drug release.