Despite much work on the neural and physiological correlates of meditation practices, little is known about how these correlates relate to altered subjective experiences known to accompany such practices. The meditation depth questionnaire (MEDEQ) measures 5 different categories of altered subjective experiences accompanying meditation graded into five levels of depths: hindrances, relaxation, personal self, transpersonal qualities and transpersonal self. In this study, we investigated the neural and physiological correlates of subjectively-experienced meditation depth across these five levels. In two groups of participants, long-term meditators (LTM) and meditation-naïve controls (CTL), we measured how MEDEQ response covaried with electroencephalography, pulse and respiration across a baseline state and two types of meditation practices. As expected, we observed that CTLs reported experiencing more hindrances than LTMs, while only LTMs reported significantly greater experiences of transpersonal qualities and transpersonal self following the two meditation practices compared to baseline. In the brain, we found that while alpha (7–13 Hz) power correlated negatively with hindrances, its correlation with subjective experience became increasingly positive as depth-level increased to transpersonal self. Theta (4–6 Hz) power however showed the exact opposite pattern with a positive correlation with hindrances and a gradually increasing negative correlation with depth-level. Brain topographies moreover revealed that deepening meditation experiences were accompanied by deactivation of theta power at different loci in the two groups—frontal midline in LTMs and frontal lateral in CTLs—corresponding to the two different aspects of executive/metacognitive processing, monitoring and regulation respectively. This supports the idea that, while critical for overcoming hindrances, metacognitive processing prevents deeper meditation experiences requiring effortless attention or meditative absorption, and that prolonged training can enable suspension of such processing at an earlier stage of processing. Meditation depth was also associated with reduced heart rate in CTLs but not in LTMs indicating that prolonged meditation training may help reduce interoceptive influences on conscious experience. While alpha and theta oscillations have been found to reliably change with meditation practice, ours is the first study to our knowledge to show how they are simultaneously related to different types and levels of subjective experiences accompanying such practices.