The aim of the present study is to evaluate the stability of DMPC:Pluronic F-127 and DPPC:Pluronic F-127 liposomes, both with and without incorporated quercetin. Quercetin belongs to the class of flavonoids and has shown antioxidant, antiviral, anti-inflammatory, anti-cancer, and antimicrobial activities. Dynamic light scattering, electrophoretic light scattering, and differential scanning calorimetry (DSC) were utilized to investigate the cooperative behavior between liposomal components and its effect on stability. All formulations were stored at 4 °C and 25 °C and studied over 42 days. Furthermore, the interaction of the final formulations with serum proteins was assessed to evaluate the potential of Pluronic F-127 as a stabilizer in these liposomal nanosystems. This study highlights the impact of DSC in preformulation evaluations by correlating thermal behavior with quercetin incorporation and variations in size and the polydispersity index. According to the results, quercetin increased the fluidity and stability of liposomal nanosystems, while Pluronic F-127 was not sufficient for effective steric stabilization. Additionally, DSC thermograms revealed the integration of Pluronic F-127 into lipid membranes and showed phase separation in the DMPC nanosystem. In conclusion, the results indicate that the DPPC:Pluronic F-127:quercetin nanosystem exhibited the desired physicochemical and thermotropic properties for the effective delivery of quercetin for pharmaceutical purposes.