Johannes Pflüger was born in Kaiserslautern, Germany. He completed his professional training as a musician at the University for Church Music (Hochschule für Kirchenmusik) in Tübingen, Germany and at the Hanover University of Music, Drama and Media (Musikhochschule in Hannover, Germany).
In 2007, Johannes Pflüger was the premier award winner of the Burkard-Steinmeyer-Orgel Improvisation Competition in Heddesheim, Germany. Additionally, he was awarded the prize of distinction at the Red-Ribbon-Award (2007) as well as at the Kleuker organ anniversary Composition Contest of the Johanneskirche (2009) competitions, both held in Saarbrücken, Germany.
He served as organist of the Christuskirche in Reutlingen, Germany from 2007 to 2009. Subsequently, from 2010 until 2014, he became cantor of the Peter and Paul Churchin Elze/Han, Germany in addition to conducting organ instruction for the protestant state church of Hanover, Germany (evangelische-lutherische Landeskirche Hannover).
In 2014, Johannes Pflüger was appointed cantor of the Friedenskirche in Bonn, Germany.