The proliferation of Internet of Things (IoT) devices has significantly expanded attack surfaces, making IoT ecosystems particularly susceptible to sophisticated cyber threats. To address this challenge, this work introduces A-THENA, a lightweight early intrusion detection system (EIDS) that significantly extends preliminary findings on time-aware encodings. A-THENA employs an advanced Transformer-based architecture augmented with a generalized Time-Aware Hybrid Encoding (THE), integrating packet timestamps to effectively capture temporal dynamics essential for accurate and early threat detection. The proposed system further employs a Network-Specific Augmentation (NA) pipeline, which enhances model robustness and generalization. We evaluate A-THENA on three benchmark IoT intrusion detection datasets-CICIoT23-WEB, MQTT-IoT-IDS2020, and IoTID20-where it consistently achieves strong performance. Averaged across all three datasets, it improves accuracy by 6.88 percentage points over the best-performing traditional positional encoding, 3.69 points over the strongest feature-based model, 6.17 points over the leading time-aware alternatives, and 5.11 points over related models, while achieving near-zero false alarms and false negatives. To assess real-world feasibility, we deploy A-THENA on the Raspberry Pi Zero 2 W, demonstrating its ability to perform real-time intrusion detection with minimal latency and memory usage. These results establish A-THENA as an agile, practical, and highly effective solution for securing IoT networks.

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