Initial excavations at the site took place from 2002 until 2004 (Permit Nos. A-3775, A-4015, A-4241). Parts of fortifications that dated to the Early Islamic period were discovered, as well as occupation remains and various finds from the Late Bronze and Iron Ages. Work was resumed in 2005 (Permit No. A-4620) and concentrated mainly in the area below the floor of the church. Large retaining and defensive walls were discovered, probably of Early Islamic date. A limited excavation was conducted in early 2006 under a small chamber built against the natural cliff at the southern end of the second floor of the complex. Reference to these earlier excavations can be found in publications relating to archaeological salvage work in the adjacent coastal promenade (HA-ESI 111:40; 114:53). The excavations reported hereafter continued the work under the church, reaching down to natural bedrock.  
The excavation area (10×10 m, depth c. 4.5 m) was divided into four squares. The bulk of the removed soil consisted of fill, intentionally deposited as part of massive earthworks that significantly altered the natural topography. The fill contained large quantities of predominantly Early Islamic pottery, dating to the eighth–tenth centuries CE. Despite variations in the soil types of the fill, the finds were consistent in volume, character and date, supporting the assumption of a single introduction episode.
More prominent architectural features (Fig. 2) were a defensive wall along the northern end of the site (W4031; width 1.5 m, preserved height c. 6 m; Fig. 3) and an opposite set of retaining walls built against the natural kurkar face, along its southern limit (W4050; Fig. 4). Both walls were founded on bedrock. Wall 4031 was split by modern development into an eastern (W4011) and western (W4121) parts. Dressed stones were used for the façades while fieldstones and hard mortar comprised the core. The lower courses, which displayed a higher degree of quality, raise the possibility of several phases of construction. The wall was probably part of Jaffa’s defenses during one of the early phases of Islamic rule.
The retaining walls against the southern rock face belonged to at least three different phases of construction. Diverse building styles and types of masonry stones were used for each wall; their orientation varied slightly, although noticeably, and each was separated from the others by perpendicular walls. The easternmost retaining wall (W4050; exposed length c. 6 m) was built of ashlars, some of them placed as headers and stretchers. It was slightly tilted southward, following the steep slope of the cliff. Its western end was disturbed and the stones were removed. A different retaining wall (W4132; length 3.8 m) was discovered to the west of W4050. It was built of large and carefully dressed blocks, bound with hard mortar.
The architectural remains exposed on bedrock created a space that was subdivided into several architectural units. Fragmentary preservation and limited exposure prevented clear determination of their plan and function; yet similarity in elevation, construction style and associated finds indicated a single phase. The northern W4031 was the limit of the excavation area in that direction. The eastern part of the complex included W4050 and a north–south perpendicular wall (W4139), whose two detached segments had survived at opposite ends. The robber trench of the central section was clearly visible. The floor to the east of the wall was covered with tightly packed crushed lime (Fig. 5). A stone-lined rectangular installation (0.7×1.5 m; Fig. 6) was built against the eastern face of W4139, near W4011. The bottom of the installation contained some ash, but its function remains unclear.
The western part of the complex occupied most of the excavation area, although only small parts, at the northern and southern extremities, were excavated to floor level. The area was limited by W4139 to the east and by another long wall to the west (W4131), which could be traced undisturbed (length 7.8 m; Fig. 7) from the retaining wall at the south (W4132) up to W4121 in the north. The western section of a probe in the corner between W4131 and W4121 revealed sloping layers of fill, poured over the horizontal surface. The beddings of the floors, laid directly over the natural rock, were also clearly discernible (Fig. 8). The complex was probably used for a variety of outdoor work functions, possibly including stone cutting, as evidenced by accumulations of dressed building stones found mainly at the southern part (Fig. 9).
The excavations under the Armenian Monastery's church suggest that significant changes were made to the northern limits of Jaffa during the Early Islamic period. The nearly vertical natural cliff face was supported by massive retaining walls, probably after suitable alterations, and the ground between the cliff and the coastline was incorporated within a new wall into the fortified urban sphere. The area adjacent to the wall was sparsely built, allowing space for work, storage, and unhindered military movement. At some stage, the whole area was filled-in with large quantities of earth. The retaining walls and the fortification were used as box frames to contain the fill. The reasons behind these changes remain obscure, as does the exact date when they took place, although the dominance of Early Islamic pottery in the fill suggests that it happened sometime between the ninth and the eleventh centuries CE. The lack of later artifacts precludes the possibility that the fill was introduced during the construction of the monastery itself in the seventeenth century CE.