Kyai Qosim later founded pesantren in Putukrejo. On the advice of Kyai Yahya Syabrowi, his boarding school was called Pondok Pesantren Raudlatul Ulum II. At the beginning of the establishment of pesantren, the ordeal came to hit Kyai Qosim. At first the existence of Kyai Qosim is often criticized by some people around pesantren. According to them, Kyai Qosim was too kemajon to establish pesantren even though in their eyes his presence in putukrejo village was considered a newcomer. 

According to the story of Mrs. Nyai Zainab, once on the day Kyai Qosim Bukhori received a letter questioning his whereabouts. According to the author's assessment of the letter as a new person in putukrejo village do not act much by setting up a pesantren. Surprisingly, according to Mrs. Nyai Zainab, although there was a letter of contents, the look on Kyai Qosim Bukhori's face was not without any change and he just said, "Yes, it's okay. Lha wong just like that."

The obstacles faced not only befall Kyai Qosim Bukhori personally, but also the santri often receive and experience some kind of physical terror. Although Kyai Qosim Bukhori was wracked with such trials, it did not appear from him any signs of anger, and annoyance. So the obstacles that befell him, he faced with a high enough level of patience without the slightest sense of resentment.

It's even been KH. Fudloli Bukhori, his brother, told him that his brother was being berated by people, but he heard and received the news. Seeing this patience, the brother then became astonished, "Why are you this? "It's people but it's still steadfast," asked Kyai Fudloli Bukhori. "I remember how the prophet's misery in fighting for Islam. What happened to me was nothing compared to what he received."  Subhanallah.