This study aimed to compare service quality and challenges faced by Local Government Units (LGUs) linked with Government Financial Institutions (GFIs) and those that are not. One hundred seventy-nine (179) LGU employees from the Fourth District of Laguna Province, were surveyed via purposive sampling. Results showed that out of the 14 municipalities included, five had linked up with LANDBANK, a GFI, while the remaining nine still needed to start linking up with GFIs, representing 64.29% of the total municipalities. The studys results found that the lack of funding for ICT infrastructure, absence of an IT officer, poor internet connectivity, and lack of knowledge in digitalization were significant challenges encountered in implementing e-payment touchpoints. The study also found that the linked LGUs scored significantly higher in the efficiency of services, fiscal benefits, process improvement, and business-friendliness than non-linked LGUs, suggesting that linking up with GFIs positively impacts service quality perceptions. The study provides insights for the GFIs sector and LGUs in improving their e-payment services and overall service quality.