Collaborative Intrusion Detection Systems are considered an effective defense mechanism for large, intricate, and multilayered Industrial Internet of Things against many cyberattacks. However, while a Collaborative Intrusion Detection System successfully detects and prevents various attacks, it is possible that an inside attacker performs a malicious act and compromises an Intrusion Detection System node. A compromised node can inflict considerable damage on the whole collaborative network. For instance, when a malicious node gives a false alert of an attack, the other nodes will unnecessarily increase their security and close all of their services, thus, degrading the system’s performance. On the contrary, if the spurious node approves malicious traffic into the system, the other nodes would also be compromised. Therefore, to detect a compromised node in the network, this article introduces a device integrity check mechanism based on “Digital Genome.” In medical science, a genome refers to a set that contains all of the information needed to build and maintain an organism. Based on the same concept, the digital genome is computed over a device’s vital hardware, software, and other components. Hence, if an attacker makes any change in a node’s hardware and software components, the digital genome will change, and the compromised node will be easily detected. It is envisaged that the proposed integrity attestation protocol can be used in diverse Internet of Things and other information technology applications to ensure the legitimate operation of end devices. This study also proffers a comprehensive security and performance analysis of the proposed framework.