•A novel scheme is proposed for IoT-based healthcare systems to generate and maintain medical certificates.•The proposed blockchain system ensures the security of medical certificates.•In the proposed scheme, the Merkle root hash of the medical certificate is maintained with a unique transaction identity.•Experimental results prove the efficiency of the proposed scheme over the existing schemes. Nowadays, blockchain technology is one of the advanced technologies to ensure the security of users’ sensitive or confidential data. Blockchain technology plays a vital role in various applications like artificial intelligence, supply chain, cloud computing, the healthcare sector, and many more. It helps the healthcare domain to get benefitted from its many advanced features, such as confidentiality, decentralization, security, and privacy. Also, the Internet of Things (IoT) devices connect with the healthcare systems, and the healthcare sector application software further communicates with the IT industry. The blockchain-based IoT systems have significantly impacted the healthcare sector by enhancing security, privacy, transparency, and efficiency, providing better business opportunities. Moreover, traditional healthcare systems face severe security and privacy problems, such as phishing, masquerades, identity theft, and many others. Thus, a secure blockchain-based Proposed Application (PA) is designed to generate, maintain, and validate healthcare certificates. The PA acts as a communication medium between the backend blockchain network and application entities like hospitals, patients, doctors, and IoT devices to create and verify medical certificates. It also ensures various security features, namely confidentiality, authentication, and access control, using the concept of smart contracts. The comparative and performance analysis of the proposed work shows that it provides a more effective solution than the existing schemes.