Father John was born on October 7, 1925, in Boston, Massachusetts, to immigrant parents Anthony John and Evangeline Karadimitriou Limberakis, who left their homeland of Alatsata, a suburb of Smyrna, Asia Minor, in 1922.

He was the eldest of four children and attended public schools in Somerville, Massachusetts. At age 16, graduating high school in his junior year, he enrolled at Holy Cross Greek Orthodox School of Theology when it was located in Pomfret, Connecticut.

Upon graduation in 1948, he was appointed registrar of the Seminary, serving as executive secretary to the late dean, the Rt. Rev. Athenagoras Cavvadas, who was also the bishop of New England.

He pursued graduate studies, first in Fresno, California, then in Providence, Rhode Island, and finally in Philadelphia. He received a Bachelor of Arts (BA) and a Bachelor of Divinity (BD) degrees from Holy Cross School of Theology and a Master of Arts (MA) degree from Temple University.