This puja mainly belongs to the Smarta sampradaya of Hinduism. It was introduced in the eighth century by Adi Shankara, who was a noted Hindu philosopher. This puja mainly consists of the worship of five deities namely, Surya, Devi, Vishnu, Ganesha and Lord Shiva. One of these deities is kept at the center and the rest of them surround it. This placement of deities mainly depends on the tradition that is followed in a Smarta household.
Apart from Smarta sampradaya, the Udasi sect also follows the tradition of Panchayatana and they mainly believe in Guru Granth Sahib, which is said to be the Sacred Text of the Sikhs. The Udasi sects have interpreted it according to the philosophy of Vedanta and for this reason they take part in Nirgun Pooja as well. They even respect aarti tradition of Sanatan Dharma.
It was noted in the role of Ishwara that an approach to god may sometimes end up in fanaticism, which is the opposite extreme end. This is not considered good at all. In Smarta sampradaya, Panchayatana puja is the one and only way to get rid of all the problems in their lives. According to this sect of Hinduism, this puja has been invented by Shankaracharya.
It is believed that many sects of people have misinterpreted the main philosophies of Hindu religion and for this reason they were completely against the Vedas. It is believed that many sects were arguing over the fact that whether lord Shiva is superior then Lord Vishnu or both of them are less superior then Mataji or Mata Parvati. This puja was started just to alleviate this debate and to make people think of the Advaita bhava.