Thomas continued his career in the church after the fall of Beaulieu and already in 1539 was made rector of Bentworth in Hampshire. In May 1548 he was also made Treasurer of Salisbury Cathedral and given the prebend of Calne while retaining his rectory. Since he could only be in one place at a time, somewhere he was an absentee incumbent. The appointment under the Protestantizing Edward VI suggests that Stevens was now of flexible theological views. At some point he married, too, and had children, who are mentioned in his will.