The monastery is consisted of two main building complexes, the Lower (Kato) Monastery of Saint John the Baptist and the Rear (Pisso) Monastery of Saint John the Theologian, which is in operation today.
The Lower Monastery had the farming installations and facilities and was the staying place mainly of the younger monks and civilian personnel. It is an irregular arrangement of buildings, situated on rough soil, within a rectangular courtyard with Saint John's church at the center, in accordance with the dominant architectural pattern of Orthodox monasteries. The main entrances to the complex are through a sculptured arcade from the courtyard side. By the north entrance is the kitchen, with an impressive tall chimney bearing the date 1816, in which stands a cooking stove. On the north side there are two-storey cells of arched chambers, each of 26 meters in length, 11 meters in height and width. The one of the chambers had openings on the walls which were used for feeding livestock. The second chamber was designed to be used as an olive - oil mill. On the southern side there is a confined atrium with six cells and further southwards warehouses on ground level for stocking goods and attics for the accommodation of the labouring personnel. Near the southern entrance the monks' workshops are located; these included a saddle- maker's shop, a carpenter's workshop, a shoemaker's workshop, a basket weaving shop and a shop for the repair of farming tools. Opposite the workshops there is a long, dining room, with an inscription (1804) appears. The abbot's quarters of two floors are on the west side of the courtyard. It comprises five cells for accommodation to official guests and at the ground floor cellars and small places for accommodating the monks.

The Church (Katholikon) in the center of the courtyard is a single nave building with an arched roof. It measures 10,5 m in length, 4,4 m in width and 6 m in height. On the west wall there is a tower for two bells and a round decorated skylight. The icons and the remaining relics which have been saved from the various loots and destructions are kept in the museum of the Rear Monastery.

The Rear Monastery ( Ground Plan) is situated at the foot of a mountain overlooking the vast blue Libyan Sea. To the left of the main entrance lies the picturesque little cemetery of the monks, which its chapel of the Holy Trinity and church - shaped ossuary. Basically the monastery has the shape of an irregular , with buildings on the north, the west and part of the east sides of a level area, with the church (Katholikon) in the center. This level area was formed partly by filling the incline with earth and partly by leaving vaulted spaces underground. At the south end of the west side stands the building which is used for official receptions and which used to house the museum before. Next to it exists a large two- floor building, opposite the Church, which houses on the ground floor the old- reception hall, dining room, the kitchen and food cellars. The upper store, incorporating simple neoclassical elements, comprises a spacious room for official meetings and smaller rooms to accommodate honoured guests.

There is an official dining - room, which is a long, flat - roofed chamber, running east to west, with a cross over its arched entrance giving the date (1804). Next to the dining room is the former hostel of the Monastery with exits to the mountains in order to make the getaway of visiting fugitives easy.
Next to that room is a furnace area which is divided into smaller sections by three high, pointed arches. In the part of the building, the oldest of the Monastery, there is a cooking stove and wooden boxes for stocking flour. At a short distance from the north-west corner of the complex there is group of ruined buildings, the cells of nuns, in which female religious (usually relatives of the monks) once lived.
On the long north side of the monastery appear series of two - store cells, the homes of the monks.
The water needs of the monastery were covered by a simply carved fountain still in use, which bears the date (1701) and an inscription. Almost directly opposite the fountain is the entrance to a long, enclosed chamber, used as a stabling unit. It has recently been turned into the new museum of the Monastery.
In tbe center of the courtyard stands the present church (Katholikon) of the Monastery, built on the side of the older, probably frescoed church which was demolished in 1835. The building of the church was delayed by the Turks and finally was completed in 1837 and was consecrated for use in the same year. Considering the facts given and the technical support at that time, the church is a large two-nave construction which is unified, internally by a sequence of three arches. The walls are 1.50m thick at the bottom and 1.20 m at the top. The building is 13.8 metres long, 10.8m width and 7.8m high, and has a simple plaster finish. On each of the two long sides two windows with high pointed arches are located. At a later date a door was inserted on the south wall of the sacrament chamber. Only the external face of the west wall has been given architectural design: a high terrace of carved, porous stone on which the bell~tower (for three bells) stands. This western facade unifies the two naves, but the end of their roofs can be seen just behind the stone cornice. The only decorative elements on this facade are the round skylights with perforated, carved lunettes and the rectangular stone cornice. The luxurious marble d0or-frames and the Byzantine double-headed eagle were put in place (according to the inscription) in 1911 during the Abbacy of Neilos Volanakis, and these replaced the much simpler door-frames of the 1835 church.
The interior of the church (Katholikon) of the Monastery of Preveli is particular interest because it has remained intact, without any later interference, except for the decorative tiles on the floor. The naves are separated by a series of three semi-circular arches supported on strong pillars which have simple capitals and bases. The blooms of the arches and the fronts have been decoratively carved and in the middle of each arch there is a sculptured emblem from which silver candles are to be hung. By the first pillar stands the carved wooden and gold-plated pulpit with its wooden stairs which twist round the adjoining pillar. The written inscription says: "This pulpit was carved by Dimitrius Ragouzis the Sikineos during the Abbacy of Daniel Koufakis in 1863. Gold-platted and icon-painted during the Abbacy of Kallinikos Spitadakis (the First in July 1874". The lower part of the pulpit is .formed by three triangular bevelled sections divided by rows of stars. Each triangular section contains floral decorations which surround two oval frames in which painted pictures of the apostles appear.
Other important items are the magnificent Patriarchal Throne, against the south wall, and the five- sided shrine of carved wood which stands next to the second pillar.
The icon of St. John the Theologian in the shrine and an icon of St. Charalambis with scenes from his life, places on the capital of the pil- lar, are the work of a very fine painter whose activity, in the years around 1830, has been traces to the region of Sfakia and Aghios Va,ssilios. The "painter of Sfakia" as we call him, repeats with considerable persuasiveness and satisfactory quality designs of the late Cretan School of painting. The icons of the iconostasis were painted by good local painters in the years 1840- 1841. During the time of the Revolution in 1866, the iconostasis and icons were taken down and hidden, with the relics and looms in nearby caves to avoid their destruction. The construction of the iconostasis is uniform across the two naves of the church and represents a complete iconographic programme which gives some independence to each nave. The architectural design and the decoration link it to the tradition of the Cretan School of Painting as it was shaped at the end of the period of the Venetian rule, mainly by competent painter on the island who adopted a popular version of the style.