Microfluidic devices offer scalable, reproducible platforms to produce liposomal drug delivery systems. Yet the relationship between flow rate ratio (FRR), drug-to-lipid (D/L) ratio, and drug encapsulation efficiency (EE%) remains incompletely defined. This study investigated the impact of FRR and D/L ratio on liposome colloidal properties and the passive loading of doxorubicin hydrochloride (DOX·HCl) using a 3D-printed T-junction microfluidic chip. Zwitterionic (DOPC) and anionic (DOPC:DOPA, 75:25 w/w) liposomes were generated at a fixed total flow rate (12 mL/min) and varying FRRs (3:20 to 1:3, organic: aqueous). Increasing FRR led to a decrease in D/L ratio, causing a significant decrease in liposome size (from ∼120 nm to ∼100 nm) and increase particle concentration (>20-fold). EE% of DOX·HCl increased with decreasing D/L ratio, reaching 4.4% in DOPC and 75.5% in DOPC:DOPA liposomes at FRR 1:3. Comparing methods to adjust D/L (adjusting FRR or total lipid concentration injected into the system) showed that while EE% remained similar, FRR adjustment significantly increased liposome concentration and resulted in less variability in liposome size and morphology. These findings demonstrate that modulating FRR in a macro-geometry microfluidic device enables precise control of liposome size, yield, and loading, without the need to increase lipid input. This work highlights the potential of low-cost 3D-printed microfluidic devices for high-throughput production of drug-loaded liposomes and underscores the critical role of FRR in optimizing encapsulation and formulation parameters.