Action to address risk and opportunities is one of major requirements in Quality Management System (QMS) based on ISO9001:2015 standards. Each of organization that certified to ISO9001:2015, the organization shall embark the risk based thinking (RBT) in their organization. The objectives of this research are to determine issues in implementation of risk-based thinking (RBT) and recommended the applied RBT framework based on case studies in three organizations. The issues determine from the case studies included 1) To many and complicated RBT approaches; 2) Not integrated the RBT with strategic and operation; 3) Communication and awareness of RBT. Based on issues determined, each organization proposed several solutions to address the issues and the solutions are compiled as the effective RBT framework.