He was a member of the Church of England and tended to favor the interests of minority religious groups in the primarily Quaker colony.
As governor, Markham helped select the site for Philadelphia, bought land from the Indians along the Delaware River and Pennsbury Manor, and began the discourse with Lord Baltimore over the disputed boundary between Pennsylvania and Maryland.
Markham had several disputes with the legislative body and issued his own version of the Frame of Government of Pennsylvania in an attempt to resolve some of this conflict.
Markham was criticised by the surveyor-general of customs and fellow Governors such as Francis Nicholson for, among other things, allowing pirates such as Thomas Day to run rampant.
Penn also complained of fraudulent financial transactions with Markham, but still had him appointed, through the deputy governor, register-general of wills in 1703.