The Sikh Panth co-existed within the framework of the Mughal Empire. The relationship was tense from the outset. Guru Nanak referred negatively to Emperor Babur's invasion of Punjab within the sacred Guru Granth scripture. The relationship deteriorated sharply by the time of Guru Arjan, who was executed by the regime. His successor Guru Hargobind stood armed at the leadership of the community with the institution of miri-piri or the power of temporal and spiritual held by the Guru. Guru Har Rai remained in the Rajasthani court, protected away from Punjab. Guru Tegh Bahadur was also executed by the regime, which ultimately led to full-scale arming and a fundamental shift within the Panth to the Khalsa, the militarisation of the Singhs. The fact leaders were being executed from an early stage indicated the Mughals deemed the community a threat. References from Mughal sources do not paint the Gurus in a good light, and descriptions even called them "bandits."

The fractious relationship lines up with the growth in the community's size but also its growth within the zamindar or land-owning classes of Punjab. Even though Sikhs were led by Khatri's ultimately, the Jatt landowners came to dominate the community. These were wealthy, well-equipped groups who could pose a serious threat to the Mughal authority. The growing numbers of followers, especially amongst these groups, were recognised by various Mughal leaders throughout the period. The structure of the Guruship also began to look more like a throne. The Gurus were militarily trained, taught multiple languages, established multiple religious sites and instructed their community through their network of masands or local community leaders throughout the subcontinent. On top of this, the language of Gurmukhi or written Punjabi, was invented by the Sikh Gurus, the establishment of a central religious text lends further to the growing problems this was causing the Mughal Islamic authority throughout the Empire.

I do not believe the Sikhs were proactively attempting to undermine Mughal authority. Rather, the Mughals perceived them as a threat due to their activities which they responded to violently, and the Sikhs replied in kind. Leading the path of full-scale war by the time of Guru Gobind Singh and Banda Singh Bahadur.