The altar lost its function at the latest in Late Antiquity, when Christianity replaced and suppressed polytheistic religions.
In the 7th century the acropolis of Pergamon was strongly fortified as a defense against the Arabs.
In the process the Pergamon Altar, among other structures, was partially destroyed in order to reuse the building material.
The city was nevertheless defeated in 716 by the Arabs, who temporarily occupied it before abandoning it as unimportant.
It was only resettled in the 12th century.
In the 13th century Pergamon fell to the Turks.

Between 1431 and 1444 the Italian humanist Cyriacus of Ancona visited Pergamon and described it in his commentarii (diary).
In 1625 William Petty, chaplain to Thomas Howard, 21st Earl of Arundel, a collector and art patron, traveled through Turkey, visited Pergamon, and brought back to England two relief panels from the altar.
These pieces were forgotten after the Earl's collection was dispersed and were only rediscovered in the 1960s.
For this reason these two panels are lacking in the Berlin reconstruction.
Other travelers known to have visited Pergamon during the late 18th and early 19th centuries were, for example, the French diplomat and classical scholar Comte de Choiseul-Gouffier, the English architect Charles Robert Cockerell and two Germans, the archaeologist Otto Magnus von Stackelberg and the classical scholar Otto Friedrich von Richter.
Choiseul-Gouffier was the first to propose excavations in Pergamon; the other three travelers made drawings of the city's acropolis.

The German engineer Carl Humann came to Pergamon for the first time in 1864/65.
He was charged with geographic investigations and repeatedly visited the city in the following years.
He urged the preservation of the antiquities on the acropolis and attempted to find partners to assist in an excavation; as a private person he was not equal to such a major task, lacking the financial and logistic resources.
It was important to begin excavation work as soon as possible because the local inhabitants of Bergama (the modern name of the ancient city of Pergamon) were using the altar and other above-ground ruins as a quarry, were looting the remnants of antique constructions in order to erect new buildings, and were burning some of the marble for lime.
In 1871 the Berlin classicist Ernst Curtius and several other German scholars came to Pergamon at Humann's invitation.
He arranged to ship some of the finds to Berlin, including two fragments of the altar frieze.
He described the reliefs as (translated) "a battle with men, horses and wild animals".
These pieces were put on display but were at first largely ignored.

Alexander Conze, who was appointed director of the sculpture collection of Berlin's royal museums in 1877, was the first person to connect the fragments with the Ampelius text and realize their significance.
The timing was good, because the German government was anxious to match the other great powers also on a cultural level after the German Empire was established in 1871:
It is very important for the museums’ collections, which are so far very deficient in Greek originals […] to now gain possession of a Greek work of art of a scope which, more or less, is of a rank close to or equal to the sculptures from Attica and Asia Minor in the British Museum.

Conze immediately contacted Humann, who at the time was in Turkey working for a road construction company.
Things then moved quickly.
The German government arranged for a license to dig in Turkey and in September 1878 excavations began, headed by Humann and Conze.
By 1886, large parts of the acropolis had been investigated and in the following years also scientifically appraised and published.
Based on an agreement between the Ottoman Empire and the German government, starting in 1879 the relief panels from the Pergamon Altar along with some other fragments came to Berlin and into the possession of the Collection of Antiquities.
The German side was well aware that by doing this a work of art was being removed from its original location and was no
The altar lost its function at the latest in Late Antiquity, when Christianity replaced and suppressed polytheistic religions. In the 7th century the acropolis of Pergamon was strongly fortified as a defense against the Arabs. In the process the Pergamon Altar, among other structures, was partially destroyed in order to reuse the building material. The city was nevertheless defeated in 716 by the Arabs, who temporarily occupied it before abandoning it as unimportant. It was only resettled in the 12th century. In the 13th century Pergamon fell to the Turks.
Between 1431 and 1444 the Italian humanist Cyriacus of Ancona visited Pergamon and described it in his commentarii (diary). In 1625 William Petty, chaplain to Thomas Howard, 21st Earl of Arundel, a collector and art patron, traveled through Turkey, visited Pergamon, and brought back to England two relief panels from the altar. These pieces were forgotten after the Earl's collection was dispersed and were only rediscovered in the 1960s. For this reason these two panels are lacking in the Berlin reconstruction. Other travelers known to have visited Pergamon during the late 18th and early 19th centuries were, for example, the French diplomat and classical scholar Comte de Choiseul-Gouffier, the English architect Charles Robert Cockerell and two Germans, the archaeologist Otto Magnus von Stackelberg and the classical scholar Otto Friedrich von Richter. Choiseul-Gouffier was the first to propose excavations in Pergamon; the other three travelers made drawings of the city's acropolis.
The German engineer Carl Humann came to Pergamon for the first time in 1864/65. He was charged with geographic investigations and repeatedly visited the city in the following years. He urged the preservation of the antiquities on the acropolis and attempted to find partners to assist in an excavation; as a private person he was not equal to such a major task, lacking the financial and logistic resources. It was important to begin excavation work as soon as possible because the local inhabitants of Bergama (the modern name of the ancient city of Pergamon) were using the altar and other above-ground ruins as a quarry, were looting the remnants of antique constructions in order to erect new buildings, and were burning some of the marble for lime. In 1871 the Berlin classicist Ernst Curtius and several other German scholars came to Pergamon at Humann's invitation. He arranged to ship some of the finds to Berlin, including two fragments of the altar frieze. He described the reliefs as (translated) "a battle with men, horses and wild animals". These pieces were put on display but were at first largely ignored. 
Alexander Conze, who was appointed director of the sculpture collection of Berlin's royal museums in 1877, was the first person to connect the fragments with the Ampelius text and realize their significance. The timing was good, because the German government was anxious to match the other great powers also on a cultural level after the German Empire was established in 1871:
It is very important for the museums’ collections, which are so far very deficient in Greek originals […] to now gain possession of a Greek work of art of a scope which, more or less, is of a rank close to or equal to the sculptures from Attica and Asia Minor in the British Museum.
Conze immediately contacted Humann, who at the time was in Turkey working for a road construction company. Things then moved quickly. The German government arranged for a license to dig in Turkey and in September 1878 excavations began, headed by Humann and Conze. By 1886, large parts of the acropolis had been investigated and in the following years also scientifically appraised and published. Based on an agreement between the Ottoman Empire and the German government, starting in 1879 the relief panels from the Pergamon Altar along with some other fragments came to Berlin and into the possession of the Collection of Antiquities. The German side was well aware that by doing this a work of art was being removed from its original location and was no
Pergamon Altar