Background: Kerala is facing challenges in the secondary prevention efforts of non-communicable diseases (NCDs). In spite of being the top performer in health parameters among Indian states, the burden of NCDs, especially diabetes mellitus (diabetes) and hypertension, is higher in Kerala. This research endeavours to identify the role of quality of medical prescriptions in secondary prevention of diabetes and hypertension and suggest corrective measures. Methods: This cross-sectional study involved collection of prescription data and other details from consenting doctors across seven districts in Kerala. After the quality of prescription was assessed using a checklist, scores were generated, and cutoff points were used to classify the prescriptions. PASW version 18 software, was used for data analysis which included univariate and bivariate analyses and logistic regression. The proportion of quality prescriptions was estimated after adjusting for clustering, and the proportion of doctors writing quality prescriptions was also estimated. Prior to the study, ethical clearance from Independent ethics committee in Health action by People (HAP) and informed consent from all the study participants were obtained. Results: After assessing 9199 prescriptions from 344 doctors, it was found that about 37.2% (95% CI: 34.9-39.4%) of the prescriptions were of good quality, and 48.2% (95% CI: 42.9-53.7%) of the doctors provided quality prescriptions. Factors associated with quality prescriptions were found to be knowledge about NCD guidelines, quality certifications of hospitals and usage of patient data management software. Conclusions: In the context of rising prevalence of NCDs and the challenges in the secondary prevention efforts, this is one of the first studies in Kerala to evaluate the quality of prescriptions to manage NCDs as prescriptions often reflect the quality of medical management. The study also addresses other factors associated with quality medical management. The findings indicate that the scope for improvement is more than 50%, when considered for the overall quality of prescriptions in diabetes and hypertension management. Further, it was found that appropriate training of doctors, adherence to treatment guidelines and the use of technology may improve the overall quality of prescriptions.