Arjan's prominence, and his community's growth, drew him into the politics of the Mughal court. When the rebel prince Khusrau fled toward the Punjab against his father, the emperor Jahangir, Arjan was accused of having blessed and aided him. He was arrested, and he died in Mughal custody at Lahore in 1606.
This is one of the more securely attested events of early Sikh history, for Jahangir records it in his own memoir, the Tuzuk-i-Jahangiri, writing that he ordered Arjan's property confiscated and the man himself put to death, a rare external corroboration, though the emperor frames it in his own terms, citing the "false traffic" of a following he wished to end. Sikh tradition remembers a death under torture and reveres Arjan as the first of the faith's martyrs.
Its effect was structural. The execution turned the Panth toward self-defence: Arjan's son and successor, Hargobind, took up arms and built a seat of temporal power, and the community that Arjan had organised as a scriptural congregation began to arm itself as a polity.