The present work is an attempt to investigate the implementation of quality system procedures on the supply chain risks in pharmaceutical companies. The risks inherent in the supply chain threaten the effectiveness and quality of the product. This paper presents a qualitative research method for analyzing the supply chain risks and for identifying ways of information support. Based on the review and data collected from the different pharmaceutical companies, awareness and traceability for the route of supply falls under the medium-risk class in most of the companies and is identified as a key risk factor. Results indicate that a thorough knowledge and well-defined quality system procedures on the supply chain flow and route of supply can mitigate the identified risks. The framework is validated with the case study based on semi-structured interviews and discussions. This provides a clear road map to the quality and supply chain managers to focus on the key risk areas. This paper contributes to research by proposing a complete approach, which integrates quality system perspective and supply chain process in a unique framework to understand the implications and to alleviate supply chain risks.