He started several public singing and scripture recital traditions in Sikhism. The katha or discourse style recitals were added by Guru Har Rai, to the sabad kirtan singing tradition of Sikhs. He also added the akhand kirtan or continuous scripture singing tradition of Sikhism, as well as the tradition of jotian da kirtan or collective folk choral singing of scriptures.

Reforms
The third Sikh leader Guru Amar Das had started the tradition of appointing manji (zones of religious administration with an appointed chief called sangatias), introduced the dasvandh ("the tenth" of income) system of revenue collection in the name of Guru and as pooled community religious resource, and the famed langar tradition of Sikhism where anyone, without discrimination of any kind, could get a free meal in a communal seating.

The organizational structure that had helped Sikhs to grow and resist the Mughal persecution had created new problems for Guru Har Rai. The donation collectors, some of the Masands (local congregational leaders) led by Dhir Mal – the older brother of Guru Har Rai, all of them encouraged by the support of Shah Jahan, land grants and Mughal administration, had attempted to internally split the Sikhs into competing movements, start a parallel guruship, and thereby weaken the Sikh religion. Thus a part of the challenge for Guru Har Rai was to keep Sikhs united.

He appointed new masands such as Bhai Jodh, Bhai Gonda, Bhai Nattha, Bhagat Bhagwan (for eastern India), Bhai Pheru (for Rajathan), Bhai Bhagat (also known as Bairagi), as the heads of Manji's.