The Chalcolithic is the phase which emerges from the Neolithic, when copper begins to be worked, farming becomes more established, and new types of pottery are produced. Chalcolithic people were experimenting with copper working in Faynan. Although their mines have been largely removed by later activity, some archaeologists have argued that the marks of Chalcolithic tools can still be seen on some rock faces.

The final phase of the pottery Neolithic site of Tell Wadi Feinan is probably Chalcolithic in date. Other Chalcolithic settlements developed into Bronze Age sites, notably the large settlement of Wadi Fidan 4.