The excavation was conducted in a streambed to the north of Nahal Kesalon, c. 20 m south of ‘Ein Naqa‘a, beside the main Emmaus–Jerusalem road that was paved in the Late Roman period (Fischer, Isaac and Roll 1996). A survey of the region discovered remains of a ruin with a stone capital (Ein Mor 2013). A previous excavation at ‘Ein Naqa‘a uncovered a water system with a hewn tunnel, a storage pool, and built and plastered channels covered with stone slabs (Storchan 2016; Golding-Meir and Cohen-Klonymus 2017). This water system was probably built by the Roman Tenth Legion in the mid-first–second centuries CE. Remains of walls and potsherds from the Roman–Byzantine periods and flint items of the Upper and Middle Paleolithic were found in the past in Nahal Kesalon, to the east of the site (Permit No. A-7281; Z. Matskevich, pers. comm.). In the center of Moshav Bet Neqofa, five settlement strata revealed in a previous excavation were dated to the Early Roman (first century BCE–first century CE), Late Roman (second–third centuries CE), Late Roman–Byzantine (third–early fourth centuries CE) and Ottoman periods (Be’eri 2015). On the southern shoulder of the road and to the southeast of the current excavation, terrace walls and two roads—one ancient and one modern—were excavated in the past (Storchan 2015). A villa, two buildings, an industrial winepress and a kiln dating from the Byzantine period were excavated c. 60 m south of the current site, on the southern shoulder of the road (Permit No. A-7786).
The current excavation comprised 22 squares in an area covering approximately half a dunam (Figs. 2, 3). It uncovered a basilica church (Fig. 3:A–H) with three construction phases, as well as a building (Fig. 3:I) and a cistern, all of which are dated to the Byzantine period (fourth–seventh centuries CE), as well as architectural remains and tombs from the Early Islamic period (seventh–eighth centuries CE; Nagar 2016; Landes-Nagar 2018). The finds were dated based on the ceramic, glass and numismatic finds. The excavation also yielded various finds, including flint items, with no stratigraphic context, which attest to a human presence at the site or in its vicinity in prehistoric periods and during Iron Age II and the Hellenistic, Roman and late Ottoman periods.
 
Byzantine Period (fourth–seventh centuries CE). The excavation uncovered a basilica church (16.7 × 17.5 m; Fig. 4) built along an east–west axis. It was poorly preserved, both because of its location in a river tributary and because two modern sewage channels cut across its center. Three construction phases were identified in the church. In the earliest phase, at the beginning of the period, a narthex (A), a nave (B), two aisles (C, D) and two anterooms (E, F) were built. The church’s walls were built of dressed stones, medium–large in size, that were preserved to a maximum height of two courses. In the middle phase, a baptisterium chapel (G) was added on, abutting the north wall of the northern part of the church. The chapel walls were carefully built of a row of medium-sized dressed stones made of soft limestone that were preserved to a height of three courses. The walls within the chapel were coated with two layers of white plaster, and its floor was paved with white mosaic. A small, plastered quatrefoil baptismal font (0.8 × 0.8 m; Figs. 5, 6), with a square basin in its center (0.45 × 0.45 m, depth 0.2 m), was installed in the chapel’s northeastern corner. Based on pottery sherds from the bedding of the mosaic floor, the chapel was built in the sixth century CE. In the latest phase, three plastered rectangular installations were built (H; 0.5–1.0 × 1.7 m), abutting the chapel on the east. The abundant flat (tegula) and convex (imbrex) tiles that were scattered throughout the compound attest to the tiled roof of the church. Based on the ceramic finds (Fig. 7), along with the glass and numismatic finds, the church was abandoned toward the end of the Byzantine period.
 
Early Islamic Period (seventh–eight centuries CE). Abutting the church on the west, east of the building, were several phases of construction remains—walls and a stone floor—with incorporated liturgical elements in secondary use that had been dismantled from the church after it went out of use. Based on glass finds from its bedding, the floor was probably laid in the Umayyad period.
Four burials in in unmarked graves were discovered in the eastern part of the excavation area. Three were inside the rectangular installations (H) of the previous construction phase; these were covered with earth. The fourth burial was discovered in a trench dug to the north of the installations. At least nine individuals were identified. They were all buried in a roughly east–west alignment, with their heads in the west, facing south. They are dated to the Umayyad period based on glass finds from one of the graves. The graves also yielded Byzantine potsherds and glassware, an orange amber bead and a metal bracelet decorated with incisions (Fig. 8).
Based on these finds, the site was probably completely abandoned sometime in the eighth century CE.
 
The church was identified by L. Di Segni with a site mentioned in the Lectionary of Jerusalem as one of the places where saint days were celebrated. This liturgical calendar was compiled in the Byzantine period (fifth–eighth centuries CE), and its copies are preserved in tenth-century CE Georgian manuscripts. The calendar states that on the fifth of July, a feast was held in honor of St. Stephen, the first martyr, at a site named Einbikumakuba (Garitte 1958:271). When divided into three (Ein–biku–makuba), the name bears a phonetic resemblance to the name ‘Ein Beit Naquba, which was phonetically and graphically corrupted through translated into different languages. In the 1920s, F.M. Abel, followed by S. Verhelst, proposed to identify the location of the church mentioned in the lectionary with the site of ‘Ein Beit Naquba near Qiryat Ya‘arim (modern-day Abu Gosh), on the ancient main road from Emmaus to Jerusalem (for references, see Nagar 2016:199).
The church was built in the fourth–fifth centuries CE and abandoned in the Late Byzantine period. During the Umayyad period, the Muslim settlement was concentrated outside the church and to its west, while the eastern part of the church precinct was used as a burial ground. The site was completely abandoned sometime in the eighth century CE. The site’s importance derives from fact that the church was dedicated to the first Christian martyr, and it is located near a spring and beside the ancient main road that connected Emmaus and Jerusalem via Abu Gosh and Moza. These attributes meant that it could provide hospitality and religious services to the numerous pilgrims and travelers on the ascent. Other pilgrim churches built beside main roads are found elsewhere in the country, such as in Judea and Samaria, and they differ from churches that were built in settlements to serve the local population (Magen 2012:1–92).