Stroke remains one of the leading causes of long-term disability worldwide, frequently leaving patients with persistent motor impairments that reduce autonomy, quality of life, and socioeconomic participation. In this context, Brain–computer interface (BCI) technologies have emerged as a promising strategy to restore sensorimotor functions by enabling patients to interact with external devices through neural activity alone. However, despite substantial technological advances, current BCI interventions still face major translational barriers because their effectiveness varies considerably across individuals and over time. A key need is therefore the development of objective and reliable biomarkers capable of monitoring task engagement, rehabilitation progress, and learning dynamics, enabling truly personalized neurorehabilitation. NETCORE addresses this challenge by investigating biomarkers derived from the interplay between the brain and the heart, an emerging research area showing that multisystem interactions provide richer and more clinically informative insights than the study of isolated organs. By combining advanced biomedical signal processing, network science, physiologically informed neural modeling, and higher-order interaction analyses, the project will develop innovative methodologies to characterize brain–heart functional circuitry during motor imagery and BCI training. NETCORE will first establish these mechanisms in healthy participants before translating the approach to stroke patients, thereby creating a pathway toward clinically relevant biomarkers for adaptive rehabilitation. Beyond technological innovation, the project contributes to a broader shift in neuroscience and healthcare toward systems-level and personalized medicine approaches, aligning with European strategic priorities in digital health, neurotechnology, and patient-centered rehabilitation. The project also integrates perspectives from cognitive neuroscience and computational modeling, disciplines at the intersection of social sciences and biomedical research, to better understand how physiological and cognitive processes jointly shape rehabilitation outcomes. By establishing novel tools to quantify multisystem dynamics, NETCORE is expected to contribute to more effective and individualized BCI therapies, while opening new avenues for understanding the role of brain–heart interactions in neurological disorders and recovery.