[2] During his presidency, Zafy received poor polling numbers due to an economic decline with accusations of corruption in his office.

[3] After leaving office, Zafy remained active in politics as an opposition leader under successive administrations.

He took office in late March–the first time since Madagascar's independence in 1960 that an incumbent president peacefully transferred power to an elected member of the opposition.

[2][10] Ravony resigned in October 1995, and Zafy appointed Emmanuel Rakotovahiny, who was the head of the UNDD and had been Minister of State for Rural Development and Land Reform, in his place.

[11][12] Zafy's time in office was widely seen as being marked by economic decline, which negatively impacted his popularity, and amid accusations of corruption and abuse of power,[2] he was impeached by the National Assembly on 26 July 1996.

[13] On 5 September, Zafy announced that he would leave office on 10 October, and he described his impeachment as a "constitutional coup d'état" that occurred as a result of his criticism of the National Assembly.

Although he could not delay his departure from office, he was able to stand as a candidate in the late 1996 presidential election called as a result of his impeachment.

[14] In his 1996 campaign, Zafy blamed the problems faced by Madagascar during his presidency on his opponents and the International Monetary Fund, and he downplayed the charges against him that had led to his impeachment.

He later alleged that the High Constitutional Court had switched the numbers for himself and Ratsiraka and said that he had not spoken of that at the time for the sake of peace.

Rajoelina included Zafy's adviser Betiana Bruno as one of 44 members of the High Transitional Authority, which he appointed on 31 March 2009.

Zafy expressed his objections to the transitional government at a press conference on 1 April, complaining that Rajoelina would not take his advice; he also said that he would seek provincial autonomy.

In the wake of the power-sharing agreement's collapse, Zafy declared on 18 December 2009, that the opposition would form its own government of national unity.

[28] Zafy died of a stroke on 13 October 2017 at a hospital in Saint-Pierre in the French overseas department of Réunion at the age of 90.