In recent times, organisations in a variety of businesses, such as healthcare, education, and others, have been using the Internet of Things (IoT) to produce more competent and improved services. The widespread use of IoT devices makes our lives easier. On the other hand, the IoT devices that we use suffer vulnerabilities that may impact our lives. These unsafe devices accelerate and ease cybersecurity attacks, specifically when using a botnet. Moreover, restrictions on IoT device resources, such as limitations in power consumption and the central processing unit and memory, intensify this issue because they limit the security techniques that can be used to protect IoT devices. Fortunately, botnets go through different stages before they can start attacks, and they can be detected in the early stage. This research paper proposes a framework focusing on detecting an IoT botnet in the early stage. An empirical experiment was conducted to investigate the behaviour of the early stage of the botnet, and then a baseline machine learning model was implemented for early detection. Furthermore, the authors developed an effective detection method, namely, Cross CNN_LSTM, to detect the IoT botnet based on using fusion deep learning models of a convolutional neural network (CNN) and long short-term memory (LSTM). According to the conducted experiments, the results show that the suggested model is accurate and outperforms some of the state-of-the-art methods, and it achieves 99.7 accuracy. Finally, the authors developed a kill chain model to prevent IoT botnet attacks in the early stage.