Van Noort served as dean of the Guild of Saint Luke from 1597 until 1602. He had problems with the Guild, which accused him of poor management of the accounts and misappropriation of materials of the Guild. The first conflict arose when van Noort used some unpainted panels in the Painter's Chamber of the Guild to create a composition he wanted to give as a present to the Guild in remembrance of his service as a deacon. Some other guild members objected to his actions and he was forced to substitute the panels and to ensure that they were painted within a year with a design approved by the Guild. The commission to paint the substituted panels did finally not go to van Noort but to Maerten de Vos. A second conflict with the Guild arose from the fact that he did not settle his accounts in time after he ceased being a deacon of the Guild.