He soon came into violent conflict with Pope Innocent II, however, when the archbishopric of Bourges became vacant. The king supported the chancellor Cadurc as a candidate to fill the vacancy against the pope's nominee Pierre de la Chatre, swearing upon relics that so long as he lived, Pierre should never enter Bourges. The pope thus imposed an interdict upon the king. Louis VII then became involved in a war with Theobald II of Champagne by permitting Raoul I of Vermandois, the seneschal of France, to repudiate his wife, Theobald II's niece, and to marry Petronilla of Aquitaine, sister of the queen of France. As a result, Champagne decided to side with the pope in the dispute over Bourges. The war lasted two years (1142–1144) and ended with the occupation of Champagne by the royal army. Louis VII was personally involved in the assault and burning of the town of Vitry-le-François. More than a thousand people who had sought refuge in the church died in the flames. Overcome with guilt and humiliated by ecclesiastical reproach, Louis admitted defeat, removed his armies from Champagne and returned them to Theobald. He accepted Pierre de la Chatre as archbishop of Bourges and shunned Raoul and Petronilla. Desiring to atone for his sins, he declared his intention of mounting a crusade on Christmas Day 1145 at Bourges. Bernard of Clairvaux assured its popularity by his preaching at Vezelay on Easter 1146.

Louis VII and his army finally reached the Holy Land in 1148. His queen Eleanor supported her uncle, Raymond of Antioch, and prevailed upon Louis to help Antioch against Aleppo. But Louis VII's interest lay in Jerusalem, and so he slipped out of Antioch in secret. He united with King Conrad III of Germany and King Baldwin III of Jerusalem to lay siege to Damascus; this ended in disaster and the project was abandoned.

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