Michael Gove has been sacked as Justice Secretary while Education Secretary Nicky Morgan also lost her job.
Both had professed a Christian faith with Michael Gove once saying Christianity informed his policy on prisons.
Nicky Morgan is an active member of the Conservative Christian Fellowship.
She said on Twitter: "Disappointed not to be continuing as Education Secretary and minister for women and equalities - two wonderful roles it's been a privilege to hold."
Mr Gove was sacked by the new Prime Minister on the second day of a round of appointments which has already seen fellow Brexiteer Boris Johnson - the man whose leadership plans he dashed - appointed Foreign Secretary.
The former Justice Secretary joins ex-chancellor George Osborne on the backbenches in a dramatic reshaping of the Cabinet team, which also saw Mr Cameron's Culture Secretary John Whittingdale, Chancellor of the Duchy of Lancaster Oliver Letwin and Health Secretary Jeremy Hunt leave the Government.
The sackings came as Ms May returned to Downing Street on Thursday morning to continue building her new Cabinet team.
In a message on Twitter, Mr Gove - who launched his own bid for the leadership but was eliminated after finishing third in last week's poll of Conservative MPs - said: "It's been an enormous privilege to serve for the last six years. Best of luck to the new government - MG."
This story is being updated.