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After graduating from St. Benedict's College at Atchison, Kansas in 1892, he attended St. Francis Seminary in Milwaukee, Wisconsin.
Mueller played college football at Benedictine College in Atchison, Kansas where he was a two-time NAIA All-American.
In 1817 his father died and John was sent to be educated at St James' monastery (Scots Benedictine College) at Ratisbon, Germany.