Dee was an intensely pious Christian, but his Christianity was deeply influenced by the Hermetic and Platonic-Pythagorean doctrines that were pervasive in the Renaissance. He believed that numbers were the basis of all things and the key to knowledge, that God's creation was an act of numbering.

Dee was a friend of Tycho Brahe and was familiar with the work of Nicolaus Copernicus. Many of his astronomical calculations were based on Copernican assumptions, but he never openly espoused the heliocentric theory. Dee applied Copernican theory to the problem of calendar reform. In 1583, he was asked to advise the Queen about the new Gregorian calendar that had been promulgated by Pope Gregory XIII from October 1582. His advice was that England should accept it, albeit with seven specific amendments. The first of these was that the adjustment should not be the 10 days that would restore the calendar to the time of the Council of Nicaea in 325 AD, but by 11 days, which would restore it to the birth of Christ. Another proposal of Dee's was to align the civil and liturgical years, and to have them both start on 1 January. Perhaps predictably, protestant England chose to spurn any suggestions that had papist origins, despite any merit they may objectively have, and Dee's advice was rejected.