Manufacturing sector is instrumental in driving economic growth of a country. With a vision for India to be a global manufacturing hub, boost the economic development and create ample employment opportunities, the Government of India has taken several steps in the past few years to strengthen the manufacturing capabilities in the country. Besides strengthening the logistic and supply chain infrastructure there is a need to build on the global quality standards and innovation culture for right positioning of Indian produce in the global supply chains. With the support of the Government initiatives, several manufacturing organizations are encouraged to focus on improving the quality of their products and processes. However, MSME organizations had to face several challenges such as limited skills, resources, awareness and lower acceptance of quality management initiatives that limit their scope of quality focus. This study discusses the implementation of a Six Sigma quality improvement project in an Indian MSME organization involved in the production of portable amplifier systems with an aim to reduce the repairs and rejections. The study provides a systematic roadmap for implementation of quality improvement projects in small scale manufacturing processes. We also illustrate an effective multi-criteria defect prioritization analysis based of Fuzzy-AHP methodology to identify the key defects to prioritize the improvement efforts. Compared to the frequency based prioritization as discussed in the literature, the proposed method prioritizes the key defect considering attributes critical to customers as well as to the manufacturer. The study also illustrates application of several quality management techniques such as cause and effect analysis, current reality tree, SIPOC analysis, and quality control charts in the DMAIC stages.