Soon after his ascension to Guruship in 1606, Guru Hargobind laid the foundation of a new temple at Amritsar; the Akal Takht. The Akal Takht was built facing Harmandir Sahib (the Golden Temple). Guru Hargobind had a throne built, and would administer Sikh affairs from here. The temporal nature of the Akal Takht balanced the spiritual nature of the Golden Temple, emphasizing the dual concepts of Miri and Piri introduced by the Guru. Guru Hargobind donned the royal regalia of a King and was known by the Sikhs as Sacha Padshah (The True King).

Guru Hargobind knew that the Sikh's would no longer take their freedom for granted, he undertook to steel his Sikhs against tyranny and oppression. The Guru now gave instructions to the Masands and to all the other Sikhs that they should make offerings in the future of horses and weapons rather than just money. The Hindus had become so weak that they could not contemplate any kind of resistance to the rulers of the date. The Sikhs did not believe in self-denial alone; they grew increasingly aware of the need for assertion also. They wielded arms and lived an active life, reared horses, rode on them, and racing and hunting became their pastimes. Guru Hargobind encouraged Sikhs in physical activity and weapons training as well as prayers. Soon an army of one thousand horses was raised. The spiritual side was not neglected. Guru Hargobind would rise long before the day dawned and after his bath in the holy tank, would go into meditation. The Guru would then join his Sikhs for prayers both in the mornings and evenings. Guru Hargobind did not want his emphasis on the temporal caused by the necessity for a war like posture to detract his followers from the spiritual ideals of Sikhism.

The Gurus military activities were soon reported to Emperor Jehangir by the ever jealous Chandu Shah, who still had an unmarried daughter on his hands as a constant reminder of the indignity hurled at him. Guru Hargobind was summoned by Jehangir and decided to go see the Emperor. Many Sikhs were apprehensive about the Guru going as they feared for his life. Before setting out for Delhi Guru Hargobind assigned the secular duties of running the Golden Temple to the honoured Baba Buddha and the spiritual instructions to the great scholar and scribe of the Guru Granth Sahib, Bhai Gurdas. Guru Hargobind then set out for Delhi accompanied by three hundred horses.

While visiting the shrine of Guru Nanak, Guru Hargobind met and received the blessings of Baba Sri Chand, Guru Nanak's son. Soon thereafter in 1613 a son was born called Gurditta. In 1617 another son was born, Suraj Mal. In 1618 a third son, Ani Rai was born and in 1620 Atul Rai was born. Finally in 1622 the last and fifth son, Tegh Bahadur was born. During the life of Guru Hargobind some of the most influential Sikhs of the time passed away. Baba Buddha passed away in 1631 at Ramdas, Bhai Gurdas in 1636 at Goindwal and Baba Sri Chand at Kiratpur in 1629. In October 1627 emperor Jahangir died and Shah Jahan ascended the throne in Delhi.

The mughal emperor Jahangir was out hunting one day in the vacinity of Amritsar. A favorite hunting hawk of the emperors flew into the camp of Guru Hargobind who was also hunting. When the emperors soldiers came to reclaim the hawk, a brief skirmish ensued and the hawk was not returned. Jahangir was so enraged that he sent an army of 7000 cavalry under the command of his general Mukhlis Khan to recover both the hawk and capture the Guru for his insolence. In the ensuing battle the Gurus forces emerged victorious after the Guru killed Mukhlis Khan in single combat with his sword. This battle took place in 1634. This battle marked a turning point as the Sikhs now turned militant under mughal persecution.

After the battle Guru Hargobind left Amritsar never to return. The Guru shifted to Kartarpur and went on to build the city of Hargobindpur on the banks of the river Beas. The local villagers who were members of the Gherar tribe were very excited, but the headman of the tribe Bhagwan Das did not want the Guru to settle there. Bhagwan Das who was friendly with the mughal authorities made derogatory remarks against the Guru, the Sikhs lost their temper and in the insuing scuffle, Bhagwan Das was killed. His son Ratan Chand went to Abdullah Khan the Subedar of Jullundur and convinced him to attack the Guru at Hargobindpur with a force of 10,000 troops. The Guru felt that he was being forced into a fight when all he wanted was to be left alone to pursue his religious pursuits. He said, "We are fighting for a righteous cause - our right to live with honour and in peace - and not for the sake of self glory or rule over others."

Trouble soon evolved among some of the Gurus troops. One of the Gurus favorite soldiers Painda Khan let the honour and gifts presented to him by Guru Hargobind go to his head. He gave the choice gifts which he had personally received to his son in law Asman Khan who also captured one of the Gurus favorite hunting hawks and refused to return it. When Guru Hargobind asked Painda Khan for an explanation he replied in a rude and insulting manner. Therefore the Guru regrettably terminated the services of Painda Khan. The disgruntled Painda Khan along with 500 troops loyal to him approached the emperor in Lahore and offered to join the imperial forces against the Guru. The emperor was pleased to have the help of such a close confidant of the Gurus. Painda Khan told the emperor that the Gurus army was only composed of poor peasants. In the year 1634 Fifty thousand troops under the command of Kale Khan and supported by Painda Khan were dispatched to attack the Sikhs at Kartarpur. When the Gurus forces heard about the impending attack, Dhir Mal the Gurus grandson sent a secret letter to Painda Khan pledging him his full support. The battle was fierce with Guru Hargobinds two sons Gurditta and Tegh Bahadur also fighting along with their father. Many great soldiers fell on the battlefield including Kale Khan. The mughal forces were decimated until among the remaining Painda Khan engaged Guru Hargobind in battle. Guru Hargobind had raised Painda Khan from a young age and loved him like a son, therefore he refused to strike the first blow. Painda Khan struck two times unsuccessfully missing the Guru both times. Painda Khan continued to taunt and insult the Guru until finally Guru Hargobind killed him with his sword. Seeing his body in the dust, Guru Hargobind clasped his old comrade in his arms and put his shield over Painda Khan's face to shade it from the scorching sun. Guru Hargobind then wept over the death of one so dear to him and prayed that God grant Painda Khan forgiveness and a place in heaven. In another part of the battlefield Baba Gurditta also wept at killing another mughal general Asman Khan who had been his childhood friend. The mughal forces were successfully routed and retreated with heavy losses although the Sikhs suffered over 700 dead.

Guru Hargobind now started training his grandson Har Rai the other son of Baba Gurditta as his natural successor. The Gurus own sons; Gurditta had passed away, Suraj Mal and Ani Rai were too worldly while Tegh Bahadur preferred solitude and meditation. Har Rai was a pious young man and Guru Hargobind proceeded to train him in the use of arms as well as spiritual matters. At the age of fourteen Har Rai was ordained by Guru Hargobind as the seventh Sikh Guru. Guru Hargobind bowed before Guru Har Rai as his successor. Soon thereafter Guru Hargobind passed away in 1644 having in his lifetime transforming the Sikhs into soldier-saints.