The return of the Islas de la Bahía and the death of Walker ended the immediate threat to Honduran territorial integrity, but other Central American nations continued to be involved in Honduran internal affairs. Guardiola was assassinated by his own honor guard in 1862, and the following decade witnessed the presidency change hands almost twenty times. General José María Medina served as president or dictator eleven times during that period, but Guatemalan intervention in 1876 drove him and his conservative supporters from power.
From 1876 until 1882, liberal president Marco Aurelio Soto governed Honduras with the support of Guatemalan strongman General Justo Rufino Barrios. Soto succeeded not only in restoring order but also in implementing some basic reforms in finance, education, and public administration.