His period in office saw several attempts to overthrow Juan Vicente Gómez (who remained the country's ultimate authority) including one by Román Delgado Chalbaud and another by Rafael Simón Urbina, both in 1929.

At the end of his presidential term (1922-1929), General Juan Vicente Gómez had decided to retire to Maracay from where he would maintain control of power as commander in chief of the Army.

One of the first measures that Pérez took when he came to power, was to sign an executive decree (11.10.1929), by which the bishop of Valencia, Monsignor Salvador Montes de Oca, was expelled from the country, which caused a public dispute with the Venezuelan ecclesiastical hierarchy and motivated the diplomatic intervention of the Apostolic Nuncio.

However, both the problem with the church and the accusations made by Congress were partly the product of political maneuvers aimed at replacing the weak figure of Juan Bautista Pérez with a representative of the new Andean generations, among whom were General José María García Velasco.

Faced with pressure, Pérez was forced to resign before Congress (13.6.1931), but despite the presidential aspirations of some figures, Gómez was re-elected with greater constitutional powers for the period 1931-1938.