Battles raged throughout the period of the Mughal Empire. Like many Central Asian armies, the Mughal army of Babur was horse-oriented. The ranks and pay of the officers were based on the horses they retained. Babur's army was small and inherited the Timurid military traditions of Central Asia. Babur did not introduce a gunpowder warfare system, instead relying on mounted archery. Babur's empire did not last long and the Mughal Empire collapsed with the expulsion of Humayun. The Mughal Empire founded by Akbar in 1556 proved more stable and enduring. Although the Mughals originated as a nomadic civilization, they grew more sedentary.
The armies of the Mughals were known for their high level of discipline and diverse personnel. They had absorbed almost all of Northern and Central South Asia. During the height of their military domination, their adversaries rarely fought frontal battles; the Maratha confederation, Ahmadnagar Sultanates, or the Rajput kingdoms were generally powerless against the Mughals ' cities and camps. They usually resorted to guerilla warfare or the Fabian strategy. By the time of Aurangzeb's reign the army still remained heavily diverse composed of Turanis (Central Asians), Persians, Afghans, and native Indians.
Babur to Humayun era In 1520, Babur raided western Punjab and subdued Lahore by 1524. He laid the foundation of the army during the First Battle of Panipat, where he employed Tulugma, encircling Ibrahim Lodi's army and forced it to face direct artillery fire, terrifying its war elephants. He achieved his final subjugation of the Rajputs in the Battle of Chanderi. In 1527, Babur again used muskets at Khanwa, where he defeated the alliance of Rana Sangram Singh of Mewar and other local rulers, and in 1529 won the Battle of Ghaghra against the remnants of the Afghan resistance.
The reign of Babur's successor Humayun was characterized by conflicts with the Sur Empire under Sher Shah Suri. After securing his throne, Humayun neutralized the threat of Ahmed Shah and annexed Gujarat, Malwa, Champaner, and the great fort of Mandu. Sher Shah, who at first remained in Agra and observed the Mughal military organization and administration, recorded how the Mughal empire military functioned. In conversation with his friend, Sher Shah remarked:
In 1535, Humayun became aware that the sultan of Gujarat was planning an assault on Mughal territories in Bayana with Portuguese aid. Humayun gathered an army and marched on Bahadur. However, instead of pressing his attack, Humayun ceased the campaign and consolidated, as Sultan Bahadur escaped and took up refuge with the Portuguese. Shortly after Humayun had marched on Gujarat, Sher Shah Suri saw an opportunity to wrest control of Agra from the Mughals . Humayun, faced with the rising threat of the Afghans in the east led by Mahmud Lodi, defeated their force at Dadrah in 1532, and besieged Chunar in September that year, then under Sher Shah's control. The siege continued for over four months to no avail. Sher Shah offered his loyalty to the Mughals on the condition that he remained in control of Chunar, and sent one of his sons as a hostage. Humayun accepted, lifting the siege in December 1532 and returning to Agra due to the rising threat of Bahadur Shah, the ruler of the Gujarat Sultanate. He refused to split his army, believing it would split his strength.
Sher Shah's hostility towards Bengal Sultanate prompted its ruler to request aid from Humayun, who in turn mobilized a Mughal army in July 1537, and advanced to Chunar. Humayun reached the fort in November 1537 and laid siege. The siege continued over six months until the fort fell, despite attempts from Rumi Khan to conquer the city. Sher Shah then led a second invasion into Bengal, seizing Rohtasgarh in March 1538, which he used to situate Afghan families and keep loot from the war. Sher Shah followed his victory at Rohtasgarh by besieging Gauda, which fell to Afghan forces in April 1538. With these victories, Sher Shah held his first coronation. Humayun refused to leave Bengal in the hands of a hostile state. Therefore, he began a march to Bengal against Sher Shah, but the march lost to poor weather conditions, with rains causing the loss of his baggage between Patna and Monghyr. Humayun eventually reached Gauda and seized it without opposition on 8 September 1538. Humayun remained at Gaur for months, stuck there due to the weather, as he restored order in the city.
At the same time, Sher Shah drove deep into his territory, seizing Bihar and Varanasi, while also recovering Chunar, and laying siege to Jaunpur with other detachments of the Afghan army, extending as far as Kannauj.
On June 26, 1539, Humayun fielded an army of 200,000 to face Sher Shah. Humayun crossed the Karmanasa River, where he was vulnerable to the Afghans. Sher Shah, seeing the fragile state, attacked the force led by Humayun at the Battle of Chausa. The Afghans surprised and routed the Mughals . Humayun escaped with his life, and the Mughals suffered over 7,000 dead, including many prominent noblemen.
Following his defeat, Humayun returned to Agra, and restored order after disturbances by his brother, Hindal Mirza. Humayun then mobilized a large force, and advanced with an army of 40,000, while Sher Shah amassed 15,000. Humayun met Sher Shah at Kannauj, with their armies mirroring each other across the Ganges river. Humayun crossed the river and began skirmishing. Amidst the fighting, many nobles hid their insignia to prevent them from being recognized, while many fled the battle. The Mughal army was defeated, and Humayun fled to Sindh. Following this victory, Sher Shah was crowned a second time on 17 May 1540 as Sher Shah, Emperor of Northern India.
After Sher Shah Suri's successor Islam Shah died in 1554, Humayun gathered a vast army with the help of Safavids. The vast majority of the army was Shi'a faith. Shaikh Ahmad described to Humayun, "My king, I see the whole of your army are Rafizi...Everywhere the names of your soldiers are of this kind. I find they are all Yar Ali or Kashfi Ali or Haider Ali and I have, not found a single man bearing the names of the other Companions."
Humayun placed the army under Bairam Khan, who led the army through the Punjab virtually unopposed. His only major battle came against Sikandar Shah Suri in Sirhind, where Bairam Khan engaged his enemy in open battle, but then quickly retreated in apparent fear. When the enemy followed, they were surprised by entrenched defensive positions and were annihilated. At the Battle of Sirhind on 22 June 1555, Sikandar Shah Suri's armies were decisively defeated and the Mughal Empire was reestablished. After Sirhind, most towns and villages welcomed the invading army as it rode to the capital. On 23 July 1555, Humayun once again sat on Babur's throne in Delhi.
Akbar era During the last stage of the conflict against Sur Empire, Akbar faced Hemu, a minister and general of one of the Sur rulers, who had proclaimed himself Hindu emperor and expelled the Mughals from the Indo-Gangetic Plains. Urged by Bairam Khan, who re-marshalled the Mughal army before Hemu could consolidate his position, Akbar marched on Delhi to reclaim it. His army, led by Bairam Khan, defeated Hemu and the Sur army on 5 November 1556 at the Second Battle of Panipat, north of Delhi. Soon after, Mughal forces occupied Delhi and then Agra. Akbar made a triumphant entry into Delhi, staying for one month. He and Bairam Khan then returned to Punjab to deal with Sikandar Shah Suri, who had again become active. In the next six months, the Mughals won another major battle against Sikander, who fled east to Bengal. Akbar and his forces occupied Lahore and seized Multan in the Punjab.
From 1556 to 1558, the Mughals conquered the city of Ajmer, the aperture to Rajputana, after the defeat and flight of its Muslim ruler. The city became the capital of Ajmer Subah who used it as a base for campaigns against Rajput rulers and, as the site of celebration when a campaign bore success. In the same year, the Mughals besieged and defeated the Sur forces in control of Gwalior Fort, a stronghold north of the Narmada river.
By 1559, the Mughals drove into Rajputana and Malwa Sultanate. However, Akbar's disputes with his regent, Bairam Khan, temporarily halted the expansion. Akbar dismissed Bairam Khan following a dispute at court in 1560 and ordered him to undertake the Hajj. He was defeated by the Mughal army in the Punjab. Akbar gave him the option of either continuing in his court or resuming his pilgrimage; Bairam chose the latter.
In 1560, Akbar resumed military operations. A Mughal army under the command of his foster brother, Adham Khan, and a Mughal commander, Pir Muhammad Khan, began the conquest of Malwa. The Afghan ruler, Baz Bahadur, was defeated at the Battle of Sarangpur and fled to Khandesh, leaving behind his harem, treasure, and war elephants. Despite initial success, Akbar was ultimately displeased with the aftermath; his foster brother retained the spoils and followed the Central Asian practice of slaughtering the surrendered garrison, their wives and children, including many Muslim theologians and Sayyids, who were descendants of Muhammad.
In 1564, Mughal forces began the conquest of Garha, a thinly populated, hilly area in central India that was of interest for its wild elephants. Akbar did not personally lead the campaign because he was preoccupied with the Uzbek rebellion, putting the campaign in the hands of Asaf Khan, the Mughal governor of Kara. Durgavati committed suicide after her defeat at the Battle of Damoh, while Raja Vir Narayan was slain at the Fall of Chauragarh, the mountain fortress of the Gonds. The Mughals seized immense wealth, including gold and silver, jewels, and 1,000 elephants. Kamala Devi, a younger sister of Durgavati, was sent to the Mughal harem.
In 1568, Akbar besieged Ranthambore Fort, a Hada Rajput stronghold in Rajasthan led by Rao Surjan Hada. After conquering Chittorgarh, Akbar aimed to solidify his rule of eastern Rajasthan. Employing cannon and tunneling, the Mughals overwhelmed the defenses, leading to Surjan Hada's surrender in March 1568. He swore allegiance to Akbar, joining the Mughal court as a noble.
In 1570, a deviant Sufism movement preaching Wahdat al-Wujud grew in Peshawar, founded by their charismatic leader Pir Roshan. The Roshani movement played an important part in politically in resisting the increasing influence of Mughals in the Afghan region as they gained popular support. Pir Roshan spent his life in conflict with the Mughals . His successors continued his struggle, capturing Ghazni city, prompting then emperor Jahangir to address the rebellion. After constant battles, the movement eventually weakened and ended.
In 1572, the Mughals annexed Gujarat and acquired its first access to the sea. Local officials informed Akbar that the Portuguese had begun to exert control in the Indian Ocean. Akbar obtained a cartaz (permit) from the Portuguese to sail in the Persian Gulf region. At the initial meeting of the Mughals and the Portuguese during the Siege of Surat, the Portuguese, recognising the superior strength, chose to pursue diplomacy. The Portuguese Governor, upon the request of Akbar, sent an ambassador to establish friendly relations. Next year at the close of 1573, Akbar sent an armed forces under Abdul Rahim Khan-I-Khana to pacify the rebellion in Gujarat. The rebels under viceroy Muzaffar soundly defeated and fled to Cambay (Khambhat), as Abdúr-Rahím Khán had been joined by Naurang Khán and other nobles with the Mughal army from Málwa, Thus prompting Muzaffar to fled to Rajpipla. As the conquest of Gujarát was completed in 1573, Akbar returned to Agra with the last Gujarat Sultán Muzaffar Shah III as a captive.