This study aimed to develop a structured model for identifying and explaining the barriers to establishing an effective internal control system in banks using the ISM–DEMATEL method. The research employed an applied, qualitative design. Data were collected through semi-structured interviews with 12 experts in banking internal control, including university faculty, supervisory personnel, and members of bank audit and risk committees. Purposive and snowball sampling were used until theoretical saturation was reached. Thematic analysis using MAXQDA identified core components, after which Interpretive Structural Modeling (ISM) and DEMATEL were applied to determine causal relationships and hierarchical structuring of the factors. The qualitative analysis revealed six main categories: organizational and structural barriers, legal and regulatory barriers, technological and informational barriers, human and skill-related barriers, process and operational barriers, and environmental and external barriers. DEMATEL showed that organizational and structural barriers possess the highest driving power, while legal–regulatory and technological–informational barriers act as linking factors. Human–skill, operational–process, and environmental–external barriers were classified as dependent factors. The ISM model demonstrated a hierarchical pattern in which environmental barriers exert the strongest direct influence on organizational structure. The results indicate that strengthening organizational and structural foundations should be the first step in overcoming barriers to effective internal control. Enhancing legal frameworks and technological infrastructures as linking factors further enables improvement in dependent factors, ultimately supporting the establishment of a robust and sustainable internal control system in banks.