On Wren's recommendation he was presented to the rectory of Bartlow, Cambridgeshire, by Charles I in 1639, the king exercising the patronage by reason of the outlawry of the patron, Henry Huddleston.
After his ejection, he lived quietly, at one time in the house of Sir Robert Shirley, 4th Baronet in Leicestershire, where he made the acquaintance of Gilbert Sheldon.
While subdean he was involved in a dispute with the precentor of the cathedral, John Featley, with regard to some capitular appointments, and was attacked by him in a tract entitled Speculum Mapletoftianum ('The Mirror of Mapletoft').
A bill in chancery was exhibited in 1662 against Sir John Wray for the restoration of the estates, and Mapletoft at his own expense rebuilt the demolished chapel and increased its revenues.
When in 1668 Anne Hyde, Duchess of York, began to waver in her allegiance to the Church of England, Mapletoft was recommended as her chaplain by Sheldon; but he was reluctant to undertake the office.