The museum occupies a building which dates from 1747. It was built by the Royal Consular Court for those officials who controlled the sluice gates of the San Cristóbal causeway/dike (or Albarradón) which ran for about two and a half miles across Lake Texcoco from the San Cristóbal Cathedral in Ecatepec to Venta de Carpio in the north of Mexico City. Since it was also the last rest house for viceroys before they arrived at the capital of New Spain from Veracruz, it was known as the House of the Viceroys too.

The Albarradón currently serves to continue the Morelos Road, and was part of the Mexico City-Laredo national highway and the former Mexico City-Pachuca highway. This construction and its surroundings, including the House of Morelos, were declared a Zone of Monuments in 2001.

Supreme Commander José María Morelos was brought to this house in secret (to prevent independence sympathizers from attempting to rescue him) on December 22, 1815. He was then shot and buried at the San Cristóbal parish church in Ecatepec, now Ecatepec de Morelos. A monument honoring this national hero was erected outside the house in 1864. After it became severely damaged, the current one was raised in 1912 and declared a historic monument in 1933.

The building opened its doors to the public as a community center in 1990, formally acquiring museum status in 1992. Its theme is the independence movement with a focus on Supreme Commander Morelos. As a community center, its spaces are available to citizens for such occasions as temporary exhibits, artistic and cultural activities, and academic events.