The Internet of Things (IoT) has experienced significant growth since its inception, representing a groundbreaking technological advancement. In essence, IoT involves the seamless integration of devices and data to automate and centralize various processes. This transformative technology is revolutionizing business operations and reshaping society as a whole. As IoT continues to evolve, the importance of detecting vulnerabilities and weaknesses becomes paramount in order to thwart unauthorized access to critical resources and business functions, which could potentially render the entire system unavailable. One prevalent threat in this context is Denial of Service (DoS) and Distributed DoS attacks. In this project, propose an innovative architecture known as Protocol Based Deep Intrusion Detection (PB-DID). To create our dataset, we gathered packets from IoT traffic and compared features from two well-known datasets: UNSWNB15 and Bot-IoT. We focused on flow and Transmission Control Protocol (TCP) characteristics. Our primary objective was to accurately classify network traffic into three categories: non-anomalous, DoS, and DDoS, while addressing issues like data imbalance and overfitting. Utilizing deep learning (DL) techniques, we achieved an impressive classification accuracy of 96.3%. This level of accuracy demonstrates the potential of our PB-DID architecture in effectively identifying and mitigating intrusion attempts in the context of IoT, thereby enhancing the security and reliability of IoT systems. Keywords—: Intrusion detection in IoT, Deep learning for intrusion detection, DoS detection, DDoS detection.