The excavation was undertaken in the wake of illicit digging in a hewn underground complex and was located near a massive decorated lintel that had previously been documented in surveys (Fig. 1).Seven phases (1–7) were identified in the excavation:
Phases 1 and 2: Remains of walls and hewn cavities dating to the Early Roman period.
Phase 3: A burial cave and remains of a basilica dating to the fourth century CE
Phase 4: Remains of a church, constructed in the third quarter of the sixth century CE and destroyed in the earthquake of 749 CE.
Phase 5: The church and adjacent structures were adapted for other purposes and continued to be used during the Abbasid period.
Phases 6, 7: Limited agricultural activity was conducted at the site in the Mamluk and Ottoman periods.
In March 2011, in the aftermath of the excavation, unknown individuals vandalized parts of the church’s mosaic floor that was exposed in the excavation. The site was subsequently covered over with sheets of geo-textile, beach sand and soil. The Israel Antiquities Authority is actively raising funds to conserve the site and open it for public visitation. 
 
Phase 1. Rock-hewn cavities and underground storerooms, which were part of aboveground structures that did not survive, were exposed. This phase is dated from the first century BCE until the first century CE, based on coins and pottery.
 
Phase 2. A hiding refuge that incorporated the underground cavities of Phase 1 was exposed (Figs. 2, 3). Similar hiding complexes were discovered at dozens of sites in the vicinity. This phase is dated to the period between the Great Revolt and the Bar Kokhba Revolt (70–135 CE).
 
Phase 3. A burial cave that was built inside one of the underground rock-hewn cavities of the previous phases was exposed (Fig. 4). Three hewn burial troughs that have a built railing and are accessed via a rock-hewn staircase from Phase 1 were discovered. A plastered wall was built between the steps and one of the troughs. A coin was discovered between its stones, dating to the second half of the fourth century CE—the reign of Constantius II. The cave was found devoid of any finds. Above the burial cave, remains of a basilica structure were discovered. It was built of local limestone, aligned northwest-southeast, and had white mosaic floors. Potsherds, the latest of which is a fragment of a Bet Natif lamp, are dated to the third–fourth centuries CE, and coins, the latest of which is dated to the fourth century CE, were discovered below the mosaic floor. It seems that the basilica structure was established in connection with the burial cave, although its nature is not entirely clear because the excavation in the area of the apse was not completed.
 
Phase 4. A church built inside the basilica structure of Phase 3, was exposed; it utilized part of the latter’s walls and columns (Figs. 5, 6). It was entered from the northwest via an atrium and an exo-nathex to very large doorways. The church included a nave (5.3×10.6 m), two aisles, an apse and two L-shaped rooms, adjacent to the apse. The aisles were separated from the nave by two parallel rows of columns, each consisting of four columns. The columns were cut of imported light gray marble and they had identical square bases and Corinthian capitals. The southwestern aisle (2.7×14.0 m) was narrower than the northeastern one. All the floors in the church were paved with beautiful colored mosaics (Figs. 7, 8). Animal depictions stand out prominently in the sections of mosaic preserved in the nave, the apse and on the raised bema in front of the apse (presbyterium); geometric designs are typical of the mosaics in the aisles. The mosaics in the apse and on the bema are composed of smaller tesserae than those used elsewhere in the mosaics, most likely due to their importance.
Two phases were discerned in the church. The mosaic floors in the nave and aisles are ascribed to the early phase (4a), as well as the room south of the apse that was paved with marble, probably due to its great importance; this is the only room in the church that had such paving. A relic was probably displayed in this room. The room northeast of the apse was also significant. Its southern wall was curved on the inside and decorated with a cornice (Fig. 9); at this spot in Phase 4a was a descent to the burial cave of Phase 3; therefore, the room can be called a martyrium. The burial cave was located underneath the apse and this seems to be the reason why the church was built. The room was entered by way of an opening in the eastern wall of the northern aisle. A considerable difference existed between the high level of the aisle floor and the low level of the room’s floor; hence, it is assumed that a wooden staircase was originally positioned there. The floor of the room was paved with white mosaic; since it was not excavated it can not be determined if it belonged to the early or later phase of the building. Based on the cornice, it seems that the southern part of the room in Phase 4a was covered with a semi-dome. Remains of red and yellow paint were traced on a layer of plaster that covered the ashlars and was preserved below the cornice. This room was evidently decorated with wall paintings.
The bema at the front of the apse was enlarged in the direction of the nave to the west in the later phase (4b); two built stairs, lined with marble, were leading to it. Based on recesses discovered in the top stair, as well as columnettes and fragments of marble chancel plaques that were found, it seems that a chancel screen was built around the bema in this phase. The building and the apse were paved with a colored mosaic. Two narrow openings allowed passage from the wings to the bema. A narrow opening was left in the chancel screen in the northern part of the bema so as to allow access to the pulpit. A fragment of the pulpit’s marble pedestal was discovered, not in situ, in the northeastern part of the nave. The opening between the northeastern aisle and the martyrium was blocked in this phase and a stone bench was built in the martyrium along their common wall. The opening leading to the tomb might also have been blocked in this phase with hard white mortar and stone slabs that were placed on the floor around the opening. These slabs damaged the edges of the white mosaic floor. A semicircular installation of plastered ceramic bricks was built in this phase next to the southern wall of the martyrium. A bench was built along the upper part of the installation. This is probably a baptismal font, deliberately built above the opening that led to the tomb. A new doorway was built in the martyrium, either in Phase 4b or Phase 5; it allowed direct entrance from outside the church to the martyrium, rather than through the aisle.
Four massive fallen pillars were discovered in the southwestern aisle. They were decorated with a Christogram, consisting of a cross with a loop at its top that together constitute the monogram of the Greek letters chi (X) and rho (P)—the first two letters of the name Christus. Recesses in these pillars are indicative of the phase when the roof above this wing was repaired. In a later phase the pillars were covered with a thin layer of white plaster that concealed the crosses (Fig. 10). This work was probably done by Muslims who also utilized the church structure.
Based on the pottery and coins, as well as the style of the capitals, columns and mosaics, the church is dated from the third quarter of the sixth century CE until its destruction in the earthquake of 749 CE.
 
Phase 5. Following the collapse of the church in the earthquake, construction was renewed in the region of the narthex and atrium and north of the ruinous building. Remains of walls belonging to rooms and installations were exposed; they were built of stones and architectural elements in secondary use, taken from the church. Ovens were discovered in several of the rooms and the ceramic finds included cooking pots from the Abbasid period. The nature of the occupation in this phase had changed dramatically. It no longer included an important public building and its meager remains made secondary use of building materials from the ruins of the church.

 
Phases 6 and 7. Only limited activity took place on the site during the Mamluk and Ottoman periods. Farming terraces were constructed south of the church, utilizing ancient stones and architectural elements in secondary use that were incorporated in their retaining walls.
 
The excavation has shown that the site was first inhabited in the Late Second Temple period. This was apparently a Jewish settlement that organized itself before the action of the Roman army to suppress the revolt. Following the destruction of the settlement during the Bar Kokhba Revolt, the place remained deserted until the fourth century CE, when the burial cave was installed at the site, which we think was deliberately left unused. It seems that a basilica structure paved with white mosaics was built in connection with the burial cave. A church was constructed inside the ancient basilica in the sixth century CE. The expensive building materials of the church, including the marble columns and the floors, show that its construction probably involved a wealthy donor, possibly the Bishop of Eleutheropolis (Bet Guvrin) or possibly some other donor working in cooperation with the bishop. Three points of ritual importance were apparently in the church, intended to draw pilgrims: the apse, the tomb below the church and the room south of the apse where relics might have been placed. The church continued to be used after the Muslim conquest. The crosses that adorned the large stone pillars were deliberately concealed by a layer of plaster.
Access to the tomb and the installation (for baptizing?) above it was altered so that the entrance no longer passed through the church. An interesting question relates to the religious affiliation of the community that used the church at this period. Is it possible that the church may have served both Christians and Muslims, together or separately? Or could it have been used by local Christians who converted to Islam? After the church was destroyed in the earthquake of 749 CE, a meager settlement was rebuilt at the site in the Abbasid period, probably in the second half of the eighth century CE or in the ninth century CE. It is unclear when and why the site was abandoned. During the Mamluk and Ottoman periods, mainly agricultural activity transpired at the site and in the surrounding area. Based on a description of the holy places on the road to Bet Guvrin that appear on the Madaba Map, U. Dahari and L. Di Segni (pers. comm.) suggested that the church at Horbat Midras probably belonged to the complex of the Tomb of Zechariah.