Abstract Objective Intuitive inquiry meditation is a unique form of Buddhist Zen/Chan practice in which individuals actively and intuitively utilize the cognitive functions to cultivate doubt and explore the concept of the self. This event-related potential (ERP) study aimed to investigate the neural correlates by which long-term practice of intuitive inquiry meditation induces flexibility in self-schema processing, highlighting the role of doubt and belief processes in this exploration. Methods Twenty experienced and eighteen beginner (...) meditators in intuitive inquiry meditation were recruited for this ERP study. The interactions of doubt and belief processes with concepts of the self and Buddha were investigated. A 128-channel electroencephalography (EEG) system was used to collect EEG data. The ERP data were processed and analyzed using EEGLAB. Results The data showed a double dissociation between beginners and experienced meditators (monks) in the concepts of the self and Buddha: intuitive inquiry meditation reduced the brain activity of beginners when viewing Buddha image but not when viewing a picture of themselves. However, in experienced meditators, intuitive inquiry meditation reduced brain activity when they viewed images of themselves but not when they viewed Buddha image. Further event-related spectral perturbation (ERSP) analysis revealed that experienced meditators had a greater theta spectral power and higher intertrial coherence (ITC), indicating that they could more flexibly modulate ongoing cognitive processes than beginner meditators. Conclusion Intuitive inquiry meditation could help beginner meditators detach from the concept of Buddha but not from that of the self. However, in experienced meditators, the opposite was true. ERSP analysis showed that only experienced meditators exhibited significant alterations in brain activity dynamics during intuitive inquiry meditation, which might enable these practitioners to become spontaneously detached from the concept of the self. These findings revealed the neural mechanism by which long-term practice of intuitive inquiry meditation can influence the doubting process and its effect on self-schema processing. (shrink)