Brain–computer interfaces (BCIs) decode neural activity into commands, yet most existing systems rely on fixed-window decoding that may result in redundant observation or unreliable predictions due to insufficient evidence. Adaptive temporal decision-making (ATDM) addresses this accuracy–time trade-off by progressively accumulating EEG evidence and deciding when to stop. However, existing EEG encoders are mainly designed for fixed-window decoding and may not provide reliable state representations under variable observation lengths. In addition, current ATDM-oriented encoders are typically tailored to specific EEG paradigms, limiting their applicability across different BCI tasks. To address these limitations, we propose ProtoTrigger, a two-stage prototype learning-based EEG state encoder for ATDM. ProtoTrigger uses prototype matching to extract stable local EEG embeddings and prototype-based attention to aggregate decision-relevant temporal evidence during progressive observation. Offline evaluations across three EEG paradigms demonstrated state-of-the-art accuracy-time trade-offs and strong generalizability across different EEG paradigms. An online human-in-the-loop augmented reality-based BCI experiment further demonstrated its real-time feasibility. These results suggest that ProtoTrigger provides a general EEG state encoding framework for efficient ATDM-based BCI systems.