Dedicated to San Isidro, a patron and a farmworker, this museum is located at the same place where he lived and died. Isidro is a saint of many miracles (the number of miracles attributed to him stands at 438), one of which is the legend of the Pozo del Milagro (well of the miracle). What happened was that after his son fell into a well, his persistent prayers caused the water level to rise, bringing his son out safely. This well has been preserved and is showcased in the museum itself, right next to the courtyard.

In addition, a chapel was built in 1663, at the spot where he allegedly died. Other than the focus on the life of Isidro, the museum also exhibits findings from local archaeological digs, which were formerly housed in the Museo Municipal. These include a 4th-century mosaic found on the site of a Roman villa, as well as maps, paintings, and photos of Madrid over the years.