Under Charles I he was continued in his chaplaincy, and on 3 July 1628 he received a dispensation to hold also the vicarage of St. Giles-without-Cripplegate, London.
They complained that, though the parish was very populous and the living worth £700 a year, Fuller was pluralist, non-resident, and a 'popish innovator.'
They alleged against Fuller's curate, Timothy Hutton, that he drank, danced and sang profane songs.
The authorities having refused his relatives' request that he might be buried in the church of St. Giles, he was interred at the upper end of the south aisle of St. Vedast, Foster Lane.
By his wife Katherine, who survived him, Fuller left three sons, William, Robert, and Gervase, and two daughters, Jane, married to Brian Walton.