Meharban, son of Prithia, wasted no time after the death of his father in informing Chandu who in turn informed the Emperor that the Guru had blessed Khusro and had promised that he would become the Emperor. The Emperor was also notified that the Pundits and the Qazis were enraged at the compilation of Adi Granth which blasphemed the worship rules of the Hindus and the prayer and fasting of the Muslims. By such accusations, Chandu induced the Emperor to summon Guru Arjan.

Emperor Jahangir writes in his autobiography:

"In Goindwal, which is on the river Biyah (Beas), there was a Hindu named Arjan, in the garments of sainthood and sanctity so much so, that he had captured many of the simple- hearted of the Hindus and even the ignorant and foolish followers of Islam, by his ways and manners, and they had loudly sounded the drum of his holiness. They called him Guru and from all sides stupid people crowded to worship and manifest complete faith in him. For three or four generations (of spiritual successors) they kept this shop warm. Many times it occurred to me to put a stop to this vain affair or to bring him into the assembly of the people of Islam.

At last, when Khusro passed along this road, this insignificant fellow proposed to wait upon him. Khusro happened to halt at the place where he was, and he came out and did homage to him. He behaved to Khusro in certain special ways, and made on his forehead a finger-mark of saffron which the Indians call Qashqa and is considered propitious. When this came to my ears and I fully knew his heresies, I ordered that he should be brought into my presence and having handed over his houses, dwelling places, and children to Murtaza Khan (Sheikh Farid Bukhari) and having confiscated his property I ordered that he should be put to death with tortures."

The following events led to the Guru's summons by the Emperor resulting in martyrdom:

To begin with, it was his elder brother, Prithi Chand who devoted his whole life to harm the Guru in every possible way. Secondly Chandu's animosity over his daughter's non-alliance with the Guru's son, is considered the main fuel. These men with jealousies in their hearts, concocted the real story of Khusro to rouse the ire of Emperor Jahangir which added fuel to the blazing fire. Along with these circumstances Guru's increasing influence to convert crowds of Hindus and Muslims, created a stir in the minds of the Pundits ( Brahmans) and the Qazis (Muslim priests). The compilation of Adi Granth was considered a serious blow to other religions. Through all these circumstances Guru Arjan fell a victim to the bigotry and inhumanity of the Mohammadan Emperor.

Before his departure to Lahore , the Guru appointed his son, Har Gobind as his successor and gave suitable instructions. He took five Sikhs, Bhai Bidhi Chand, Bhai Langaha, Bhai Piara, Bhai Jetha, and Bhai Pirana, with him. Some writers say that Emperor Jahangir had gone to Kashmir before the arrival of the Guru in Lahore .

The Emperor Jahangir addressed the Guru, "Thou art a saint, a great teacher, and a holy man; You look on all, rich and poor, alike. It was therefore, not proper for you to give money to my enemy Khusro." The Guru replied, "I regard all people, whether Hindu or Musalman, rich or poor, friend or foe, as equals; and it is on this account that I gave your son some money for his journey, and not because he was in opposition to you. If I had not assisted him in his forlorn condition, and so shown some regard for the kindness of thy father, Emperor Akbar to myself, all men would have despised me for my heartlessness and ingratitude, or they would have said that I was afraid of you. This would have been unworthy of a follower of Guru Nanak."

The Guru's reply did not sooth Jahangir's feelings and he ordered him to pay two lakhs of rupees (two hundred thousand rupees), and also to erase the hymns in his Granth which were opposed to the Hindu and Muslim religions. The Guru replied, "Whatever money I have is for the poor, the friendless and the stranger. If you ask for money, you may take whatever I have; but if you ask for it by way of fine I shall not give you even a penny, because a fine is imposed on the wicked worldly persons and not on priests and saints. As regarding the erasure of hymns in the Adi Granth, I cannot erase or alter an iota. I am a worshipper of the Immortal God. There is no monarch save Him; and what He revealed to the Gurus, from Guru Nanak to Guru Ram Das, and afterwards to myself, is written in the holy Granth. The hymns contained in the Adi Granth are not disrespectful to any Hindu incarnation or any Mohammadan prophet. It is certainly stated that prophets, priests, and incarnations are the handiwork of the Immortal God, Whose limit none can find. My main object is to spread the truth and the destruction of falsehood; and if, in pursuance to this objective, this perishable body is to depart, I shall account it great good fortune."

The Emperor left and the Guru was placed under the surveillance of Chandu. Some writers say that Guru Arjan's execution was nothing except usual punishment of revenue defaulter. It seems that these writers are totally ignorant of Sikh tradition. When the Sikhs of Lahore came to know about the fine of two lakhs of rupees, they decided to raise the money to discharge the Guru's obligation of fine. The Guru issued a stern warning to his Sikhs that whosoever contributed to pay the fine imposed on him, would not be his Sikh. It was a matter of principle as mentioned in the Guru's reply above, and not a matter of two lakhs of rupees which could have been collected in twinkling of an eye. Fines are for thieves, robbers, slanderers and the wicked. Men devoted to religion did not belong to that category. It is, t herefore, baseless to say that Guru's execution was usual punishment of revenue defaulter. The Qazis and Brahmans offered alternatives to the Guru to exchange death for expunging the alleged objectionable passages in Adi Granth and inserting the praises of Mohammad and of the Hindu deities. The Guru did not budge from his position.

Guru Arjan was made to sit on the red hot iron pan and burning sand was poured over his bare body. He was seated in red-hot caldron, and was bathed in boiling water. Guru's body was burning and was full of blisters.