Undoubtedly, the supply chain management (SCM) system is an important part of many organizations worldwide; over time, the technologies used to manage a supply chain ecosystem have, therefore, a great impact on businesses’ effectiveness. Among others, numerous developments have been made that targeted to have robust supply chain systems to efficiently manage the growing demands of various supplies, considering the underlying requirements and main challenges such as scalability, specifically privacy and security, of various business networks. Internet of things (IoT) comes with a solution to manage a complex, scalable supply chain system, but to provide and attain enough security during information exchange, along with keeping the privacy of its users, is the great inherent challenge of IoT. To fulfill these limitations, this study designs and models a scaled IoT-based supply chain (IoT-SC) system, comprising several operations and participants, and deploys mechanisms to leverage the security, mainly confidentially, integrity, authentication (CIA), and a digital signature scheme to leverage potentially secured non-repudiation security service for the worst-case scenario, and to leverage privacy to keep users sensitive personal and location information protected against adversarial entities to the IoT-SC system. Indeed, a scaled IoT-SC system certainly opens new challenges to manage privacy and security while communicating. Therefore, in the IoT-SC system, each transaction writes from edge computing nodes to the IoT-SC controller is thoroughly examined to ensure the proposed solutions in bi-directional communication, and their robustness against adversarial behaviors. Future research works, employing blockchain and its integrations, are detailed as paces to accelerate the privacy and security of the IoT-SC system, for example, migrating IoT-centric computing to an immutable, decentralized platform.