Scriptures state that the Lord accepts the worship of a devotee after he has become a pure as the Lord, both spiritually and physically. Hence prior to the pooja each devotee must bathe.

Verses 50 to 57 of the Shikshapatri state the main stages of this pooja.

After the ritual cleansing, the devotee should sit cross legged facing North or East and perform mansipooja (mentally contemplate) to the glory of Lord Swaminarayanbapa Swamibapa. Once the tilak chandlo has been done, he should place the murtis of Lord Swaminarayanbapa Swamibapa in front of him and recite the aavhan (welcoming) mantra.

Applying Tilak-Chandlo

Offerings of food, neyved, for prasad are placed in front of the murti and then concentrating solely on the Lord's murti, becoming totally engrossed in the murti of Lord Swaminarayanbapa Swamibapa, the devotee should recite the Swaminarayan mantra, and turn over a bead on a mara, rosemary beads, after each mantra.

Doing the mara

After completing at least three full mara while seated, the devotee should complete at least one mara while doing tapni (penance) mara. The devotee stands on his left leg, with the right leg in front of the left knee, in the crane position.

Performing the tapni mara

Pradikshina (circling the murti) is the next ritual. Inside the murti of Lord Swaminarayanbapa Swamibapa are all the great pilgrimage sites. During the pradikshina the devotee visits these sites and with each step, the sins of the devotee are destroyed. While completing pradikshina at least one kirtan should be sung. Pradikshina are symbolic of the devotion of the disciple unto the Lord.

Performing the Pradikshina

After pradikshina, the male devotees will prostrate before the Lord with the following eight parts of the body all focused to Lord Swaminarayanbapa Swamibapa; 

Head, chest, hands, knees and legs should be touching the ground. The eyes should see only the murti of Lord Swaminarayanbapa Swamibapa, while his speech is uttering prayers to the Lord. His mind should be contemplating the murti of Lord Swaminarayanbapa Swamibapa. This is called saastaang dandvant pranaam - eight fold prostration.

The female devotee will complete the same, but in a crouched position, with her hands on the ground and obviously her feet touching the ground. Again her eyes see only the murti of the Lord, while she says her prayers to Lord Swaminarayanbapa Swamibapa. Her mind should be contemplating the murti of Lord Swaminarayanbapa Swamibapa. This is called paanchaang pranaam - five fold prostration.

Once seated after the prostrating, neyved is offered to the Lord and 'Jhamo Thaar Jeevan Javu Vaari' is sung and the devotee should perform aarti. The devotee should then pray to Lord Swaminarayanbapa Swamibapa to protect and look after him during the day. After the reciting of the Visranjan (culmination) mantra, the devotee does a final darshan of the murti and then folds them away. 

Reading the Shikshapatri

Lord Swaminarayanbapa Himself commanded that each of His disciples must read at least five shloks (verses) from the Shikashapatri each day. Also at least one chapter from the great holy scriptures, the Vachanamrut and Shree Abji Bapashreeni Vato.