The puja begins with invoking a sangha as mentioned above. This is followed by the three prostrations performed by the sadhaka or dharma student. The three prostrations signify the three gates or three aggregates,which are the body, the speech and the mind. At an esoteric level they also signify the identification of the student with the three bodies of the Buddha: Dharmakaya, the sambhogakaya and the nirmanakaya .

These prostrations are also known as the five point prostrations in which five parts of a student's body touch the ground - the two palms, the two knees and the forehead. Again, an explanation at the esoteric level suggests the affinity of the five points to the five skandhas or five elements of earth, water, fire air and space, the five wisdoms emanating from the five Buddha families, the five poisons and the five Buddha energies.

Therefore, through the act of prostration the student has to invoke all these considerations and then surrender himself to Buddhas of the three times (past, present, and future) and ten directions. Even the folded hands in supplication which prostrating possesses deeper symbolism. The ten fingers touching each other signify the ten directions. The right hand stands for the male, active, yang energy while the left hand stands for the female, receptive, yin energy. Together they give rise to the Buddha's enlightening activity of upayakaushalya in which both wisdom and bliss are harmoniously blended for the benefit and ultimate enlightenment of all other sentient beings.

These offerings to the deities and the three Jewels can be followed by the Bodhisattva vows, the 100-syllable Vajrasattva mantra, mandala offerings, and the seven-line prayer of Guru Rinpoche and mon-lam prayers . Subsequent to this the devotee or supplicant can practice meditation on shunyata or emptiness. The prayers are concluded by rejoicing in the good deed and merit of others, requesting the Buddhas to teach and not enter in parinirvana. Dedications of the merit accumulated by us as a result of these prayers are then dedicated to all sentient beings.