Tel Tsaf was first identified in the 1940’s as el-Sufuh in a Beth Shean Valley survey conducted by N.Tzori. Later, as a result of the exposure of some painted pottery shards during the demolition of part of the hill, Prof. R. Gophna excavated on the main tel from 1978-1980 on behalf of the Institute of Archaeology, Tel Aviv University and the Israel Department of Antiquities. The excavation explored an area of about 100 m². During this expedition, a 2.5 meters deep probe was dug in one of the squares and hit virgin soil. From these trenches, Gophna suggested there were two occupation periods at Tel Tsaf. He attributed the earlier phase to the Pottery Neolithic period and the later and main phase to the Early Chalcolithic period. The Pottery Neolithic occupation was identified through two pits that were found dug into virgin soil in square D5. The Early Chalcolithic occupation however was much richer and showed ample evidence for mudbrick architecture and other installations. Between the two occupation layers was a layer of sandy soil. In addition to architecture, quantities of pottery, flint, ground stone tools, bones, and other organic material were exposed.

 Between 2004 and 2007, Prof. Y. Garfinkel conducted new excavations at the site. The large scale excavations (about 800 m²) were conducted in three areas on the tel. Area B is located on the western part of the site where a deep well was exposed. Area C is in the eastern part of the main hill. This part included Gophna’s area which Garfinkel named area A. The third area is D, a small probe northwest of area C. Garfinkel attributes the occupation period in areas B and C to the Middle Chalcolithic period, postdating the Wadi Rabah culture (Late Neolithic/Early Chalcolithic) and preceding the Ghassulian period (Late Chalcolithic period). A recent study of the C14 dates from this excavation was published, suggesting that Areas B and C were contemporaneous and date to the last quarter of the 6^th millennium BC and the first quarter of the 5^th millennium. According to this study, the site was abandoned during the first quarter of the 5^th millennium. During these four seasons of excavation, a large complex of four buildings and many silos, roasting pits, ovens and other installations were discovered in Area C (ca. 700 m were explored here to a maximum depth of ca. 1 m). Most architectural features were made of sun-dried mudbricks. 19 silos of various sizes were discovered in various numbers per courtyard. Because of their large size and number, the silos are a critical issue in Tel Tsaf. They show a surplus accumulation at a scale unknown in any other contemporaneous site in the southern Levant. 16 oval pit installations dug into the ground were exposed in the courtyards. These pits are interpreted as cooking facilities or earth ovens. Large quantities of animal bones were found in and around them.
Four burials were found in or in relation to the silos. The burials are of two infants and two adults. One of the adults is a woman exposed in silo C555 with a necklace comprised of 1,668 ostrich egg-shell beads placed on the frontal part of the pelvis. In the fill of this grave, situated in the northeast corner of the courtyard of Building I, a copper awl was discovered. This suggests cast metal technology was introduced to the southern Levant as early as the late 6th millennium Cal BC.