The proliferation of Internet of Things (IoT) devices has brought about an increased threat of botnet attacks, necessitating robust security measures. In response to this evolving landscape, deep learning (DL)-based intrusion detection systems (IDS) have emerged as a promising approach for detecting and mitigating botnet activities in IoT environments. Therefore, this paper thoroughly reviews existing literature on botnet detection in the IoT using DL-based IDS. It consolidates and analyzes a wide range of research papers, highlighting key findings, methodologies, advancements, shortcomings, and challenges in the field. Additionally, we performed a qualitative comparison with existing surveys using author-defined metrics to underscore the uniqueness of this survey. We also discuss challenges, limitations, and future research directions, emphasizing the distinctive contributions of our review. Ultimately, this survey serves as a guideline for future researchers, contributing to the advancement of botnet detection methods in IoT environments and enhancing security against botnet threats.