The adoption of IoT in a multitude of critical infrastructures revolutionizes several sectors, ranging from smart healthcare systems to financial organizations and thermal and nuclear power plants. Yet, the progressive growth of IoT devices in critical infrastructure without considering security risks can damage the user’s privacy, confidentiality, and integrity of both individuals and organizations. To overcome the aforementioned security threats, we proposed an AI and onion routing-based secure architecture for IoT-enabled critical infrastructure. Here, we first employ AI classifiers that classify the attack and non-attack IoT data, where attack data is discarded from further communication. In addition, the AI classifiers are secure from data poisoning attacks by incorporating an isolation forest algorithm that efficiently detects the poisoned data and eradicates it from the dataset’s feature space. Only non-attack data is forwarded to the onion routing network, which offers triple encryption to encrypt IoT data. As the onion routing only processes non-attack data, it is less computationally expensive than other baseline works. Moreover, each onion router is associated with blockchain nodes that store the verifying tokens of IoT data. The proposed architecture is evaluated using performance parameters, such as accuracy, precision, recall, training time, and compromisation rate. In this proposed work, SVM outperforms by achieving 97.7\% accuracy.