Meditation training is proposed to enhance mental wellbeing by modulating neural activity, particularly alpha and theta brain oscillations, and autonomic activity. Though such enhancement also depends on the quality of meditation, little is known about how these neural and physiological changes relate to meditation quality. One model characterises meditation quality as five increasing levels of “depth”: hindrances, relaxation, concentration, transpersonal qualities and nonduality. We investigated the neural oscillatory (theta, alpha, beta, gamma) and physiological (respiration-rate, heart-rate, heart-rate variability) correlates of self-reported meditation depth in long-term meditators (LTM) and meditation-naïve controls (CTL). To determine the neural and physiological correlates of meditation depth, we modelled the change in slope of the relationship between self-reported experiential degree at each of the five depth-levels, and the multiple neural and physiological measures.CTLs reported experiencing more hindrances than LTMs, while LTMs reported more transpersonal qualities and nonduality compared to CTLs, confirming the experiential manipulation of meditation depth. We found that in both groups, theta (4–6 Hz) and alpha (7–13 Hz) oscillations were related to meditation depth in a precisely opposite manner. Theta amplitude positively correlated with hindrances, and increasingly negatively correlated with increasing meditation depth levels. Alpha amplitude negatively correlated with hindrances, and increasingly positively with increasing depth levels. The increase in the inverse association between theta and meditation depth occurred over different scalp locations in the two groups—frontal-midline in LTMs and frontal-lateral in CTLs—possibly reflecting downregulation of two different aspects of executive processing—monitoring and attention regulation, respectively—during deep meditation.These results suggest a functional dissociation of the two classical neural signatures of meditation training, namely, alpha and theta oscillations. Moreover, while essential for overcoming hindrances, executive neural processing appears to be downregulated during deeper meditation experiences.