In the last three decades of the eighteenth century, the Order experienced a steady decline. This was a result of a number of factors, including the bankruptcy that was a result of Pinto's lavish rule, which drained the finances of the Order. Due to this, the Order also became unpopular with the Maltese.

In 1775, during the reign of Francisco Ximénez de Tejada, a revolt known as the Rising of the Priests occurred. Rebels managed to capture Fort St Elmo and Saint James Cavalier, but the revolt was suppressed and some of the leaders were executed while others were imprisoned or exiled.

In 1792, the Order's possessions in France were seized by the state due to the French Revolution, which led the already bankrupt Order into an even greater financial crisis. When Napoleon landed in Malta in June 1798, the knights could have withstood a long siege, but they surrendered the island almost without a fight.