The vast increase of Internet of Things (IoT) technologies and the ever-evolving attack vectors have increased cyber-security risks dramatically. A common approach to implementing AI-based Intrusion Detection Systems (IDSs) in distributed IoT systems is in a centralised manner. However, this approach may violate data privacy and prohibit IDS scalability. Therefore, intrusion detection solutions in IoT ecosystems need to move towards a decentralised direction. Federated Learning (FL) has attracted significant interest in recent years due to its ability to perform collaborative learning while preserving data confidentiality and locality. Nevertheless, most FL-based IDS for IoT systems are designed under unrealistic data distribution conditions. To that end, we design an experiment representative of the real-world and evaluate the performance of an FL-based IDS. For our experiments, we rely on TON-IoT, a realistic IoT network traffic dataset, associating each IP address with a single FL client. Additionally, we explore pre-training and investigate various aggregation methods to mitigate the impact of data heterogeneity. Lastly, we benchmark our approach against a centralised solution. The comparison shows that the heterogeneous nature of the data has a considerable negative impact on the model's performance when trained in a distributed manner. However, in the case of a pre-trained initial global FL model, we demonstrate a performance improvement of over 20% (F1-score) compared to a randomly initiated global model.