This study aims to analyze the implementation of the internal control system (ICS) over the credit granting process at Bank Prisma Dana Manado and to identify weaknesses that contribute to the occurrence of non-performing loans, drawing on the COSO (2013) five-component internal control framework and Agency Theory as the theoretical foundation. The study employs a descriptive qualitative method with a single case study approach on one working capital debtor who defaulted on their loan. The case was purposively selected because it represents a pattern of control weaknesses consistent with the increasing trend of Bank Prisma Dana Manado's Non-Performing Loan (NPL) ratio during the 2020–2024 period. Data were collected through semi-structured interviews with three key informants, observation, and documentation of credit policies, then analyzed using the interactive model of Miles et al. (2014), comprising data reduction, data display, and conclusion drawing/verification, and were further strengthened through source and technique triangulation. The results show that Bank Prisma Dana Manado's ICS formally incorporates all five COSO components, yet its implementation remains inconsistent, particularly in the control activities component (incomplete verification of the 5C principles) and the monitoring component (delayed post-disbursement monitoring, as well as insufficient segregation of duties between the marketing and credit analysis functions). These weaknesses directly contributed to the occurrence of the non-performing loan examined in this study and are consistent with the bank's rising NPL ratio, which increased from 5.0% in 2020 to 7.0% during 2023–2024. This study contributes to enriching the literature on internal control in Rural Banks (BPR), a segment that remains relatively understudied compared to commercial banks, while also offering practical implications for bank management and regulators in strengthening credit verification policies, segregation of duties, and post-disbursement monitoring to mitigate the risk of problem loans.