On April 13, 1634, the Mogul army attacked Guru Hargobind Sahib here. From 1635 to 1698, Amritsar remained in the control of the Mina family (descendants of Pirthi Chand). During this period, on November 23, 1664, Guru Tegh Bahadur Sahib visited the town. In April 1698, Bhai Mani Singh was appointed as the caretaker of the shrines of Amritsar.

The Mogul chief of Patti tried to occupy Amritsar several times. One such attempt was made in April 1709. The Sikhs, under the command of Bhai Mani Singh and Bhai Tara Singh of Dall-Wan, repelled this attack. When Baba Banda Singh Bahadur occupied several areas in the Punjab, Bhai Mani Singh chose to leave Amritsar in order to avoid the Mogul attacks.

On December 30, 1711, the Mogul emperor, Bahadur Shah, granted Ajit Singh Palit the charge of Amritsar in order to use him against Baba Banda Singh Bahadur. After the death of Bahadur Shah, Ajit Singh Palit returned to Delhi. In 1721, Bhai Mani Singh returned to Amritsar and re-started regular worship. His first act was to solve a dispute between so-called Tat Khalsa and so-called Bandai Khalsa for the right to the management of the shrines at Amritsar.

On March 29, 1733, a major gathering of the Sikhs was held here in front of Akal Takht Sahib. During the same time a Sarbat Khalsa gathering was also held. It discussed the Mogul offer of Nawab-hood. In April 1734, Bhai Mani Singh was arrested and was martyred at Lahore on June 24, 1734.

In 1740, Massa Ranghar, a debauched official, desecrated Darbar Sahib. He was punished by Bhai Sukkha Singh and Bhai Mahtab Singh, on August 11, 1740. In 1757 Afghan army demolished Darbar Sahib and Akal Takht Sahib. Baba Dip Singh led several thousand Sikhs against the Afghan. A major battle was fought on November 11, 1757. Baba Dip Singh and several thousand Sikhs embraced martyrdom. Again, in 1762, the Darbar Sahib complex was demolished by Afghan army. On December 1, 1764, the Afghan army made another attack. 30 Sikhs, led by Jathedar Gurbakhsh Singh, fought against mammoth Afghan army and embraced martyrdom. In 1765, the Sikhs began re-construction of the shrines. The central part was ready by 1776. Around 1830, Ranjit Singh gold-plated some part of the inner section of the Darbar Sahib. (It harmed this Sikh institution as some ignorant people began unjustly calling it Golden Temple).

In 1846, the British established themselves in the Lahore Darbar, with a Resident in the Court; and, Amritsar became a place of frequent visits by the British. In order to keep sanctity of the city, H. M. Lawrence, the British Resident, issued an order, dated March 24, 1847, asking the English people to follow the Sikh protocol while visiting the Sikh centres. In 1858, a Municipal Committee was set up here. In 1862, train services between Lahore and Amritsar were started. Khalsa College, the first Sikh college was established here in 1892. [In 1969 Guru Nanak University was established here]. In 1913, the city was electrified. In September 1915, the British declared Amritsar a "Holy City". (This order was undeclaredly annulled after August 15, 1947 by the Indian regime). On April 13, 1919, General Dyer opened fire on the gathering, at Jallianwala Bagh, near Darbar Sahib, killed 379 people and wounded another 1200. The the Shiromani Gurdwara Parbandhak Committee (S.G.P.C.) and the Shiromani Akali Dal were established here in 1920.