The first section to come into conflict with the Mughal Empire was the Jats of the Agra-Delhi region who were living on both sides of the river Yamuna.
The Jats were mostly peasant cultivators, only a few of them being zamindars. With a strong sense of brotherhood and justice, the Jats had often come into conflict with the Mughals.
The conflict with the Jats had taken place during the reigns of Jahangir and Shah Jahan on the issue of collection of land revenue.
All the imperial road to the Deccan and the western seaports passed through Jats’ area; therefore, the Mughals had to take a serious action against the Jat rebellions.
In 1669, under the leadership of local Zamindar Gokla, the Jats (of Mathura) were rebelled, which spread rapidly among the peasants of the area. This rebel compelled Aurangzeb to take serious action in person. Resultantly, the Jats were defeated and Gokla was captured and executed.
In 1685, under the leadership of Rajaram, there was a second rebel of the Jats. This time, Jats were better organized and adopted the methods of guerilla warfare, combining it with plunder.
The rebels were continued to 1691, when their leader Rajaram and his successor, Churaman, were compelled to surrender. In spite of this, unrest among the Jat peasants were remained persistent and their plundering activities made the Delhi-Agra road unsafe for travelers.
During the 18th century, taking advantage of Mughal civil wars and weakness Churaman carved out a separate Jat principality in the area and to oust the Rajput zamindars.
The conflicts with Afghans (who lived in mountain region) were continued and most of the Mughal Emperors fought with Afghans.
Akbar fought against the Afghans and in the war, he lost the life of his close friend and very intelligent and loyal noble, Raja Birbal.
The conflicts with Afghans were partly economic and partly political and religious in character.
To clear the Khyber Pass and crush the uprising, Aurangzeb deputed the Chief Bakhshi, Amir Khan. After the hard battles, the Afghan resistance was broken.
In 1672, there was a second Afghan uprising. Akmal Khan was the leader, who proclaimed himself king and struck khutba and sikka in his name.
Near Khyber Pass, the Afghans suffered a disastrous defeat; however, Khan managed to escape.
In 1674, Shujaat Khan, a Mughal noble suffered a disastrous defeat in the Khyber. However, he was rescued by a heroic band of Rathors sent by Jaswant Singh.
In the middle of 1674, Aurangzeb himself went to Peshawar and stayed there till the end of 1675. Slowly, by force and diplomacy, the Afghan united front was broken, and peace was restored.
The Sikhs were the last to come into military conflict with Aurangzeb; however, the reasons for the conflict were political and personal rather than religious.
The Gurus had started living in style, with an armed following, and assumed the title of sachha padshah (the true sovereign).
There was no conflict with the Sikh Guru and Aurangzeb, upto 1675 until Guru Tegh Bahadur was arrested along with his five followers, brought to Delhi, and executed.
The cause of Tegh Bahadur’s execution was not clear. Some Persian accounted that Tegh Bahadur had joined hands with Hafiz Adam (a Pathan) and created nuisance in Punjab. On the other hand, according to Sikh tradition, the execution was due to intrigues (against the Guru) by some members of his family who disputed his succession.
Some of the historians had written that Aurangzeb was annoyed because of the Tegh Bahadur’s act of converting a few Muslims into Sikh and raised a protest against religious persecution in Kashmir by the local governor.
Whatever the reasons, Aurangzeb's action was unjustified from any point of view and betrayed a narrow approach. Further, the execution of Guru Tegh Bahadur compelled the Sikhs to go back to the Punjab hills. It also led to the Sikh movement (led by Guru Govind Sindh) gradually turning into a military brotherhood.
Guru Govind Singh had a considerable organizational ability. By using his skill, in 1699, he founded the military brotherhood popularly known as the “Khalsa.”
Guru Govind Singh had made his headquarters at Makhowal or Anandpur located in the foothills of the Punjab. In given period of time, the Guru became too powerful.
Guru Govind fought a series of wars against the hill rajas and won. The organization of the khalsa further strengthened the hands of the Guru in this conflict.
In 1704, an open breach between the Guru and the hill rajas took place, as the combined forces of a number of hill rajas attacked the Guru at Anandpur.
The rajas had again to retreat and forced the Mughal government to intervene against the Guru on their behalf.
Aurangzeb was concerned with the growing power of the Guru and had asked the Mughal faujdar to punish the Guru.
The Mughal forces attacked at Anandpur, but the Sikhs fought bravely and beat off all assaults and they were taken shelter inside the fort.
The Mughals and their allies now captured the fort closely that closed all sorts of movements. Resultantly, starvation began inside the fort and the Guru was forced to open the gate apparently on a promise of safe conduct by Wazir Khan. But when the forces of the Guru were crossing a swollen stream, Wazir Khan's forces suddenly attacked.
Two of the Guru's sons were captured, and on their refusal to embrace Islam, they were beheaded at Sirhind. Further, the Guru lost two of his remaining sons in another battle. After this, the Guru retired to Talwandi.
Jahangir continued Akbar's policy of giving favors to the leading Rajput rajas and of entering into matrimonial relations with them.
Shah Jahan also maintained the alliance with the Rajputs, but he did not appoint any Rajput raja as the governor of a province, and no further matrimonial relations were made with the leading Rajput rajas. In spite of the fact that he (Shah Jahan) himself was the son of a Rajput princess.
Perhaps, the alliances with the Rajputs had become so consolidated, that it was felt that matrimonial relations with the leading rajas were no longer necessary. However, Shah Jahan accorded high honor to the heads of the two leading Rajput houses, namely Jodhpur and Amber.
Raja Jaswant Singh, the ruler of Marwar, was in Shah Jahan’s favor. Both he and Jai Singh held the ranks of 7000/7000 at the time of Aurangzeb's accession.
Aurangzeb secured the active support of the Maharana of Mewar and raised his mansab from 5000/5000 to 6000/6000.
Jaswant Singh who had been deputed to look after the affairs of the Afghans in the north-west died by the end of 1678.
In November 1679, Aurangzeb attacked Mewar. A strong Mughal detachment reached Udaipur and raided the camp of the Rana who had retreated deep into the hills to conduct a harassing warfare against the Mughals.
The war Between the Mughals and Rajputs soon reached at a stalemate as the Mughals could neither penetrate the hills, nor deal with the guerilla tactics of the Rajputs.
Over a period of time, the war became highly unpopular. Prince Akbar, the eldest son of Aurangzeb, tried to take advantage of the situation and he went against his father.
In January, 1681, Prince Akbar, in alliance with Durgadas, the Rathor chief, marched towards Ajmer where Aurangzeb was helpless, as all his best troops were being engaged elsewhere.
Prince Akbar, however, delayed and Aurangzeb was able to stir up dissensions in his camp by false letters. Resultantly, Prince Akbar had to flee to Maharashtra.
Aurangzeb patched up a treaty with Rana Jagat Singh (the successor of Rana Raj Singh).
The new Rana was forced to surrender some of his parganas in lieu of iazyah and was granted a mansab of 5,000 on a promise of loyalty and not supporting Ajit Singh, but it did not benefit much.
Aurangzeb’s policy towards Marwar and Mewar was clumsy and blundering, which brought no advantage of any kind to the Mughals. On the other hand, Mughal failure against these Rajput states damaged Mughal military prestige.
The breach with Marwar and Mewar weakened the Mughal alliance with the Rajputs at a crucial period.
