Antibiotic resistance is one of the most serious health challenges worldwide. In this study, nanoliposomal encapsulations of doxycycline with enhanced antibacterial effects were prepared using the modified freeze-drying of a monophase solution and two loading techniques (passive and pH-gradient) simultaneously. Different liposomes were prepared and characterized in terms of size, zeta-potential, polydispersity-index, morphology, ATR-FTIR, Powder X-ray Diffraction, and encapsulation-efficiency (EE). MICs and time–kill-experiments were performed according to CLSI guidelines. The liposomes were nano-sized and spherical in shape. The EE of the selected formulation was 37.4 ± 5.8%. The MICs were two-fold lower than those of equivalent free drugs. Nanoliposomes at 4 × MIC revealed a rapid killing of Staphylococcus epidermidis by achieving complete bacterial death at 8 h versus 16 h for the free drug. Taking five aspects (homogeneous and nano-sized liposomes, sterilization not necessary, suitable EE, and antibacterial effects) into consideration, our modified preparation method seems promising and may be used to overcome bacterial resistance. Graphical abstract: Nanoliposomal doxycycline was made via modified freeze-drying of a monophase solution. Passive and pH-gradient drug-loading resulted in suitable encapsulation efficiencies. Sterile and homogeneous nanoliposomes with good antibacterial effects were obtained. The minimum inhibitory concentrations decreased two-fold. This technique may be used to overcome bacterial resistance to doxycycline. [Figure not available: see fulltext.]