Shiva Samhita presents chakras and nadis as the essential architecture of the subtle body, through which prana, or vital energy, is directed and refined. The nadis are described as an extensive network of subtle channels, numbering in the tens of thousands, with particular emphasis on three: Ida, Pingala, and Sushumna. Ida is associated with a lunar, cooling quality and flows on the left, while Pingala is solar and heating, flowing on the right. Sushumna, running centrally along the axis of the body, is regarded as the most crucial channel for spiritual realization, extending from the base of the spine to the crown of the head. Ordinary mental activity is linked with prana moving primarily through Ida and Pingala, and yogic practice is portrayed as a process of purifying these channels so that prana may enter Sushumna. When blockages in the nadis are removed through disciplines such as pranayama, mudra, bandha, and meditation, both physical health and spiritual clarity are said to be enhanced.

Within this subtle framework, the chakras are depicted as lotus-like centers of consciousness situated along the Sushumna. The text aligns with the familiar tantric model of seven principal chakras: Muladhara at the base of the spine, Svadhisthana in the genital region, Manipura at the navel, Anahata at the heart, Vishuddha at the throat, Ajna between the eyebrows, and Sahasrara at the crown of the head. These centers are described as padmas, or lotuses, each with petals, associated letters, deities, and elements, functioning as psychic and spiritual loci rather than gross anatomical structures. Particular importance is given to the lower centers as the seat of kundalini and to the heart and brow centers as focal points for meditation and inner sound. Sahasrara, the thousand-petalled lotus at the crown, is portrayed as the supreme center where kundalini unites with Shiva, bringing about liberation.

The dynamic relationship between chakras, nadis, and kundalini forms the heart of the text’s yogic vision. Kundalini-shakti is said to lie dormant in the Muladhara, and the entire discipline of hatha and tantric yoga is oriented toward awakening this power and guiding it upward through Sushumna. As kundalini ascends and “pierces” each chakra, practitioners are described as experiencing inner light, inner sound, bliss, and a progressive withdrawal from ordinary sensory entanglement. The culmination of this ascent at Sahasrara is characterized as the union of Shiva and Shakti and the realization of a nondual reality, where the distinctions that ordinarily define experience fall away. In this way, the chakra–nadi system is treated not as an end in itself, but as a skillful means for transforming consciousness and recognizing the one, undivided ground of being.