The roots of the conflict lay in the long-standing political instability in Honduras. The nation, since its independence, had been plagued by frequent changes in government, often through military coups. President General Miguel Dávila, who came to power in 1907, faced opposition from various quarters, including former President Manuel Bonilla, who was a popular figure and had served as president from 1903 to 1907.

The civil war began in 1909 when Manuel Bonilla, supported by various factions dissatisfied with Dávila's rule, initiated a military campaign against the government. Bonilla, who had the backing of some sections of the military and the populace, posed a significant challenge to Dávila's authority.

The civil war in Honduras attracted the attention of the United States, which had significant economic and strategic interests in Central America. The U.S. government, under the presidency of William Howard Taft, was particularly concerned about the stability in the region, which was crucial for the construction and operation of the Panama Canal. The U.S. involvement often took the form of diplomatic interventions and, at times, direct military action, under the guise of protecting American interests and citizens in Honduras.

Over the course of two years, the conflict saw various battles and skirmishes, causing substantial loss of life and property. The instability severely affected the nation's economy and disrupted everyday life. Both sides faced difficulties in maintaining support and resources, with the war becoming increasingly unpopular among the general populace.

The protracted nature of the conflict and external pressures, especially from the United States, eventually led both parties to seek a resolution. In 1911, an agreement was reached to hold an election, which would be recognized by both sides as the legitimate means to resolve the presidency. This was a significant development, as it indicated a move towards a more democratic resolution of the conflict, albeit under the shadow of foreign influence.

The election, held in 1911, resulted in a victory for Manuel Bonilla. His win was seen as a repudiation of Dávila's policies and a preference for Bonilla's leadership style and policies. Bonilla's presidency, however, was short-lived as he passed away in 1913. Nevertheless, the election marked the end of the civil war and ushered in a brief period of stability.