He was gentle by nature and had a devout temperament. He was Guru Hargobind's favourite grandchild, and he had been given the name of Har Rai by the Guru himself. Once, record old texts, Har Rai was returning home after his riding exercise. From a distance he saw Guru Hargobind sitting in the garden. He at once got off his horse to go and do him homage.In this hurry, his robe was caught in a bush and a few of the flowers were broken from their stems. This pained Har Rai's heart. He sat down on the spot and wept bitterly. Guru Hargobind came and consoled him. He also advised him: "Wear your robe by all means, but be careful as you walk. It behoves God's servants to be tender to all things." There was a deeper meaning in the Guru's words. One must live in this world, and yet be master of oneself.

Guru Hargobind knew Har Rai to be the fittest to inherit the "light" from him. He nominated him as his successor and consecrated him Guru before departing this life on 3 March 1644. Guru Har Rai kept the stately style Guru Hargobind had introduced. He was attended by 2,200 armed followers, but no further conflict with the ruling power occurred. He established three important preaching missions called bakhshishes for the spread of Guru Nanak's teaching. First was that of Bhagvan Gir, renamed Bhagat Bhagvan, who established missionary centres in eastern India. The second was that of Sangatla, renamed Bhai Pheru, who preached in Rajasthan and southern Punjab. Guru Har Rai also sent Bhat Gonda to Kabul, Bhai Nattha to Dhaka and Bhai Jodh to Multan to preach. The ancestors of present-day families of Bagarlan and Kaithal preached in the Malva region. Guru Har Rai himself travelled extensively in this area and a large number of people accepted his teaching. He confirmed the blessing earlier bestowed by Guru Hargobind on a poor boy, Phul, who became the founder of the families of Patiala, Nabha and Jind. These families ruled in their territories in the Punjab until recent years.

Kiratpur was Guru Har Rai's permanent seat. Here disciples and visitors came to seek blessings and instruction. The Guru kept the daily practice of his predecessors. The institution of langar, community eating, continued to flourish. Guru Har Rai chose himself the simplest fare which was earned by the labour of his own hands. In the morning, he sat in the sangat and explained the Sikh doctrine. He did not compose any hymns of his own, but quoted those of his predecessors in his discourses. He often repeated to his followers the following verses of Bhal Gurdas,Varan (XXVIII. 15):

A true Sikh rises before the night ends,
And turns his thoughts to God's Name,
To charity and to holy bathing.
He speaks humbly and humbly he walks,
He wishes everyone well and he is joyed to
give away gifts from his hand.
He sleeps but little,
And little does he eat and talk.
Thus he receives the Guru's true instruction .
He lives by the labour of his hands and he does good deeds.
However eminent he might become,
He demonstrates not himself.
He sings God's praises in the company f holy men.
Such company he seeks night and day.
Upon Word is his mind fixed,
And he delights in the Guru's will.
Unenticed he lives in this world of enticement

Guru Har Rai was at Goindval when Dara Shukoh, heir apparent to the Mughal throne, entered the Punjab fleeing in front of the army of his brother, Aurangzab, after his defeat in the battle of Samugarh on 29 May 1658 At Goindval, where he arrived in the last week of June 1658, he called on Guru Har Rai, and sought the consolation of his blessing The prince was of a liberal religious disposition, and had a natural inclination for the company of saintly persons He was especially an admirer of the famous Muslim Sufi, Mian Mir, who was known to the Sikh Gurus Sikh tradition also recalls how Dara Shikoh had once been cured of a serious malady with herbs sent to hint by Guru Har Rai in his affliction now he readily took the opportunity of having an audience with the Guru According to Sarup Das Bhalla, Mahima Prakash, Guru Har Rai deployed his own troops to delay Aurangab's army which was pursuing Dara close at his heels.

Guru Har Rai left Goindval on a tour of the districts where the Sikh faith had taken root in the time of his predecessors. He travelled further on to Kashmir. The Baisakhi of 1660 was celebrated at Sialkot in the home of Nand Lal Puri, grandfather of Haqiqat Rai, the martyr The journey was resumed in the company of Sikhs such as Makkhan Shah, the Lubana trader, and Aru Ram, father of Kirpa Ram Datt who later led to the presence of Guru Tegh Bahadur group of Kashmiri pandits driven to dire distress by State persecution Guru Har Rai arrived at Srinagar, via Martand, on 19 May 1660, and visited Mota Tanda, the village to which his disciple, Makkhan Shah belonged. On his way back, he stopped at Akhnur and Jammu. At the latter place, the local masand, Bhat Kahna, waited on him with the sangat.