Baitoa was previously settled by indigenous peoples of the Caribbean known as Taínos for hundreds if not thousands of years prior to the arrival of Christopher Columbus in Hispaniola in 1492.

However, the Spanish Conquistadors did establish a nearby fort and settlement in La Vega, Dominican Republic in 1494, in order to mine gold.

By the mid-1700s, perhaps the 1760s, Baitoa was settled by Francisco Espaillat y Virol (1734–1807), a Frenchman, physician, and slaveholder who established sugar plantations, tobacco fields, and cattle ranches in the region.

Throughout the 18th-19th centuries, farmers from the Cibao formed semi-autonomous agricultural economies, and became increasingly involved in growing and selling tobacco to the international market, especially to Hamburg, Germany.

In the early-1800s, migration to Baitoa was probably stimulated by the Peace of Basel (1795), whereby Spain had ceded Santo Domingo to France, and by the Haitian Revolution (1791–1804), where thousands of Dominicans left the island or moved to rural communities in order to escape the reach of colonial powers and foreign rule.

By the late-1800s, more families began migrating to Baitoa from other areas of the Dominican Republic, due to the growing agricultural economy and availability of land in the region.

There are parish records that go as far back as 1863 in Santiago de los Caballeros, which affirms the presence of several growing and newly arriving families in Baitoa.

For much of the 19th-20th century, Baitoa was scarcely populated, with no more than several thousand people, and with a small number of core families who continued to form bonds and marital relationships with members of the same community.

The Espaillat came from France, the Perez and Genao came from nearby López and Angostura (which was later incorporated into Baitoa), the Pineda came from San Cristobal, the Fernández came from Puñal, the Valerio came from La Zanja, and finally, the Núñez and Franco came from Arroyo Hondo.

He was the son of Justo Franco Diaz and Maria Francisca Núñez Fernández, who were originally from Arroyo Hondo, Santiago.

The current mayor or alcalde of Baitoa is Bernardo Ernesto López Rodriguez (2016–2024), following Rádhames Rojas (2010–2016), and Jose Rafael Peña, among others.

On June 28, 2017, the Mayor of Baitoa, Bernardo López, organized a protest in front of the national palace, demanding a clean water supply system for his constituents.

The Catholic Church in Latin America plays a very important role in the culture and identity of Dominicans, especially natives of Baitoa, who come from traditional, rural families.

Prior to the opening of Iglesia San Ramon in the early 20th-century, people from Baitoa would often receive visits from parish priests from the Santiago Apostol Cathedral, located about 25 km away.

This event is a local spin off the religious holiday, El Día de San Juan (or the Day of Saint John).

Born in Baitoa, Santiago in the Dominican Republic as one of seven children, Justice Pineda-Kirwan was nine years old when she moved to New York to join her family, who had previously emigrated there.

After graduating from Jamaica High School, Justice Pineda-Kirwan went on to attend Queens College, even though her family had already returned to the Dominican Republic.