Blockchain is the most prominent phenomenon of the technological world and provides a foundation for future ecosystems to build trust less nodes in a distributed system. However, the security and privacy provided by the blockchain-based systems in industrial and business applications are not yet matured. Therefore, the security and privacy of the domains are under future researches. This paper presents and highlights the security and privacy feature in Blockchain-based systems, specifically in supply chain management, trade digitization, and smart factories. We referenced some real-life use cases of Blockchain in the supply chain, letter of credits, trade digitization, and in Smart factories. We focus on recent challenges while adding security in these systems with the blockchain and suggests some solutions to these challenges. The existing framework and merging a private block with a robust privacy guideline, following confidentiality, integrity, and availability (CIA). The traditional blockchain smart factory includes sensing layer, management hub layer, storage, firmware, and application layer, therefore, incorporating the Hyperledger Fabric with our new secure communication and storage architecture will enhance security and privacy in blockchain-based smart factories.