The museum was designed by architect Juan Navarro Baldeweg and houses the Neocueva, a meticulous reconstruction of the original cave's most celebrated chamber. Pedro Saura and Matilde Muzquiz, professors at the Complutense University of Madrid specializing in photography and drawing respectively, created the replica using the same materials and techniques employed by Paleolithic painters: ochre, charcoal, hematite, and animal fat. They studied every centimeter of the original ceiling, tracing the contours of each bison, each horse, each abstract symbol. The project demanded years of close observation, and that intensity paid an unexpected dividend. During their sustained examination of the originals, Saura and Muzquiz identified paintings and engravings that previous researchers had missed entirely. The act of copying revealed what centuries of looking had not.

Beyond the replica cave, the museum's permanent exhibition, titled Times of Altamira, walks visitors through the world that produced the paintings. Objects recovered from Altamira and other Paleolithic caves of Cantabria fill the galleries: stone tools shaped by hands that also created art, bone implements that speak to daily survival alongside the creative impulse. Artifacts from the cave of El Juyo and other nearby sites provide context for a culture that stretched across the region. The museum also offers prehistoric technology workshops where visitors can try their hands at the techniques of flintknapping and pigment preparation, collapsing the distance between tourist and Ice Age artisan into the space of an afternoon.

The museum exists because of a tension that afflicts cultural heritage worldwide: the desire to share a treasure with the public versus the need to protect it from that same public. Altamira was completely closed in 1977 after damage from visitor traffic became undeniable. A limited reopening in 1982 created a waiting list that stretched for years. When green mold appeared on some paintings in 2002, the cave was sealed again. In December 2010, the Spanish Ministry of Culture confirmed that the original cave would remain closed indefinitely, a decision based on expert analysis showing that conservation conditions had stabilized only after visitors were excluded. The museum and its Neocueva now serve as the primary way most people will ever experience Altamira's art. For the paintings themselves, silence and darkness have become their best preservatives.

As one of Spain's National Museums, the Altamira center has grown into a custodian of regional prehistory far beyond the famous cave. Its collections include materials from archaeological sites across Cantabria: the caves of El Castillo in Puente Viesgo, the cave of Chufin, the cave of La Pila in Miengo, and outdoor Paleolithic sites scattered through the countryside. The museum sits near the medieval town of Santillana del Mar, itself a destination of cobblestone streets and Romanesque architecture. The juxtaposition is striking: a twelfth-century town preserving a museum that preserves a replica of a cave that preserves the memory of people who lived here 15,000 years ago. Each layer of preservation is an act of faith that what came before matters enough to protect.