The Internet of Things has become a cutting-edge technology that is continuously evolving in size, connectivity, and applicability. This ecosystem makes its presence felt in every aspect of our lives, along with all other emerging technologies. Unfortunately, despite the significant benefits brought by the IoT, the increased attack surface built upon it has become more critical than ever. Devices have limited resources and are not typically created with security features. Lately, a trend of botnet threats transitioning to the IoT environment has been observed, and an army of infected IoT devices can expand quickly and be used for effective attacks. Therefore, identifying proper solutions for securing IoT systems is currently an important and challenging research topic. Machine learning-based approaches are a promising alternative, allowing the identification of abnormal behaviors and the detection of attacks. This paper proposes an anomaly-based detection solution that uses unsupervised deep learning techniques to identify IoT botnet activities. An empirical evaluation of the proposed method is conducted on both balanced and unbalanced datasets to assess its threat detection capability. False-positive rate reduction and its impact on the detection system are also analyzed. Furthermore, a comparison with other unsupervised learning approaches is included. The experimental results reveal the performance of the proposed detection method.