From the presence of the flint mines of Rijckholt (also present elsewhere in the municipality) it can be deduced that the area was already inhabited in prehistoric times. Traces of Roman presence are fairly rare, although according to Heerlen archaeologist Karen Jeneson, the South Limburg plateaus were also cultured during the first centuries of the Christian era. The discovery in 2012 of a settlement with wooden houses from Roman times in Eckelrade seems to confirm this statement. At Cadier en Keer the Roman villa Backerbosch is only partially excavated, but it is clear that this was one of the largest villae rusticae in the Netherlands. The Oude Akerweg in Bemelen – passing through the Wolfshuis to the Heerstraat near Scheulder – was probably part of the Roman road that led from Maastricht to Aachen. Even in the Middle Ages this road was still important, as evidenced by the presence of a guesthouse of the chapter of Sint-Servaas in the hamlet Gasthuis. The villages in the Meuse valley date from the Early Middle Ages and are older than the villages on the plateau. Breust and Eijsden are the oldest centers here. The Plateau of Margraten was only (re) mined quite late (12th-13th century).

The territory of the current municipality of Eijsden-Margraten was a patchwork of shredded territories until 1794. The large number of castles, particularly in the Meuse valley, still bear witness today to the rivalry that prevailed at the time. A few villages formed more or less independent delights within the Holy Roman Empire, such as the Gronsveld estate, the free bourgeois kingdom of Breust and the Wijlre glory, to which Scheulder belonged. The area Lord and Times belonged to the so-called Eleven banks of Sint-Servaas, which were administered by the Sint-Servaaskapittel in Maastricht. In the village of Bemelen another Maastricht chapter, that of Our Lady, acted as a lordly lord, while in the neighborhood of Antoniusbank the Maastricht Antonites were in charge. Other parts of the municipality of Eijsden-Margraten belonged to the county of Dalhem (Mheer, Banholt, Noorbeek, Cadier and Oost-Maarland) or the land of ‘s-Hertogenrade (Margraten), while a small area was part of the duchy of Limburg. In the Party Tributary of 1661, some of these territories were split up into a State part and a Spanish, later Austrian part.

The arrival of the French in 1794 put an end to the fragmentation and from 1814 the area belonged successively to the United Kingdom of the Netherlands (1814-30), the Kingdom of Belgium (1830-39) and from 1839 to the Kingdom of the Netherlands. The larger villages (Eijsden, Gronsveld, Margraten, Mheer, Noorbeek, Sint Geertruid and Bemelen) each formed a separate municipality until 1982. During the reorganization of South Limburg on 1 January 1982, the municipalities Eijsden and Margraten were formed, which merged on 1 January 2011 to form the current municipality.

In 2016, the municipality agreed with the Belgian town of Wezet to exchange two pieces of territory that had ended up on the other side of the Maas by a diversion of the river in the 1970s, forgetting a border correction. The peninsulas L’Illal and Eijsden of 15 hectares become Dutch, the Dutch peninsula Petit-Gravier of 5 hectares Belgian. The decision was made because of law enforcement problems on L’Illal.

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