In April 1983 the organization faced a serious internal crisis with the assassination of Mélida Anaya Montes (Commander Ana María) in Managua, Nicaragua.

The Secretary General and leader of the organization, Salvador Cayetano Carpio was accused of ordering the assassination, and committed suicide before the investigations into her death concluded.

[6]: 253  Although the FPL initially claimed the kidnapping was done for ideological reasons a randsom demand of US$20 million was made for his release.

It initially adhered to rigidly communist principles and believed that only rural insurgency could be successful, but grew more pragmatic over time and became willing to work together with the FMLN.

[1] The organization also followed liberation theology, to the point that the Salvadoran security forces believes that the FPL was formed by progressive Jesuits.