During the English Civil War Captain Ellis defended the castle for four years for the king with his own private funds after the death of the bishop.
While in college he received several anonymous donations for his father's suffering during the Civil War and to fund Ellis' education.
Around the time his book "The Gentle Sinner; or England's Brave Gentlemen" in 1660 he became the rector of the parish of Kirkby-in-Ashfield.
Through his charitable work and his church sermons he was able to help bring about unity to the parish that had been lost during the Civil War.
However, again not wanting to leave his congregation in Kirkby and also because of his ailing health prevented him from fulfilling all of his duties he decided to resign his preferment.