The third son of Ferdinand Maria, Elector of Bavaria and his wife, Princess Henriette Adelaide of Savoy, Joseph Clemens was designated by his parents for a life in the church.

He became Archbishop of Cologne in 1688 after the death of Maximilian Henry of Bavaria, and his appointment to that post by Pope Innocent XI was one cause of the Nine Years' War.

Joseph Clemens was the younger brother of Maximilian II Emanuel, Elector of Bavaria.

[1] As did his brother, Maximillian II, Joseph Clemens allied with France during the War of the Spanish Succession and was forced to flee his residence Bonn in 1702 and found refuge at the French court.

The war between France and the Holy Roman Empire was finally ended in 1714 with the Treaty of Baden, which restored Joseph Clemens.