Galindo's father was a government official in Costa Rica. He was of Spanish, English and Irish descent, but the curious rumor that Juan Galindo was actually born in Ireland as "John Gallager" seems to be false.
Galindo worked for the government of the United States of Central America (see: History of Central America). In addition to his military duties, he wrote accounts of local conditions, topography, and landmarks. He explored a number of ruins of the Maya civilization, including Palenque and Copan, and wrote descriptive accounts. Galindo's publications attracted the attention of US writer John Lloyd Stephens, prompting Stephens' more detailed investigation of the area's ruins.
Galindo's writing on the Maya sites are notable as the first pointing out that the persons depicted in Maya art looked like the local Maya people, and saying that the modern Maya are probably the descendants of the builders of the ancient monuments. At the time, and even later, many other writers attributed the ancient monuments of America to such peoples as Egyptians, Polynesians, or the Lost Tribes of Israel.
Colonel Galindo was a loyal supporter of the liberal central government of President Francisco Morazán. When civil war broke out in Central America, he fought in various battles. He was killed when a conservative army from Nicaragua took the city of Tegucigalpa.