In late February 2012, just four months after he assumed office, Prime Minister Garry Conille resigned. The resignation came after weeks of tension with President Martelly. Conille was Martellys third choice for the position after Parliament rejected his first two nominees. Conille decided to resign after he called a meeting with his cabinet ministers and none of them attended. Conilles exit came at a time when Haiti was still recovering from the devastating 2010 earthquake. In early 2012, half a million Haitians were still living in tents. Also in early 2012, seven Haitian police officers were convicted in the prison massacre that happened a week after the 2010 earthquake. The officers were charged with murder, attempted murder, along with various other crimes. They received sentences ranging from one to 13 years in prison.

On April 12, 2012, cholera vaccines began, eighteen months after the outbreak of the disease. More than 7,000 Haitians have been killed and more than 530,000 have been infected with the disease. The delay in the vaccine was largely political. Finally, a national bioethics committee approved the vaccination plan, which will reach only about 1 percent of the population and uses the cheapest cholera vaccine available. A second round of vaccines was scheduled for late April. Organizers of the vaccine were racing against the seasonal rains, which spread the disease. On May 3, 2012, Laurent Lamothe was approved as Haitis new prime minister by the Chamber of Deputies. The vote was 62-3 in favor of Lamothe.

In late August 2012, Tropical Storm Isaac hit Haiti with rains and winds that caused flooding and mudslides. According to the civil defense authorities, at least four people were killed, including a ten-year-old girl who died when a wall collapsed in Thomazeau. The storm did not cause the kind of widespread damage initially feared. However, the storm was the latest obstacle for a nation still recovering from the devastating 2010 earthquake.