The Benaki Museum's collection of post-Byzantine ecclesiastical art comprises a selection of sacred and service vessels, liturgical vestments, jewellery and accessories, and church furnishings in carved wood. It covers a chronological period spanning from the 16th century, when the Orthodox Church began recovering from the Ottoman conquest, to the start of the 20th century.

The origin and workmanship of the objects in the collection represent the wide geographical spectrum within which the Greek cultural presence made itself known: Pontos, Cappadocia, Transylvania, Wallachia, Venice and Russia. An important part of the collection is made up of heirlooms brought to Greece by refugees from Asia Minor and Eastern Thrace and kept at the Benaki Museum on a permanent basis. Objects for ecclesiastical use are made out of precious and semi-precious materials such as silver, gold, gems, silk, and gold thread, and often bear dedicatory inscriptions naming the donor or patron who commissioned them, the artistan who created them, and the date and place where they were produced. The donors of such items usually belonged to the higher strata of society, which was represented during the period of Ottoman rule by the ecclesiastical authorities and the local notables. Intended to enhance the authority of the Church, post-Byzantine ecclesiastical art preserved traditional Byzantine forms and iconography, while at the same time reflecting artistic influences derived from the great urban centres of the East and West.

The Benaki Museum's collections of neo-Hellenic secular art, which cover the chronological period from the fall of the Byzantine Empire in 1453 to the end of the 19th century, are thought to be unique in terms of their outstanding quality, number and variety. They are witness to both the common elements and the local variations evident in the neo-Hellenic artistic expression, in areas as diverse as the Frankish-occupied territories of Crete, Cyprus and the Dodecanese and Ionian Islands, and the Ottoman-occupied areas of Pontus, Asia Minor, Thrace, Constantinople, Macedonia, Epirus, Attica and the Peloponnese.

Wood carving and sculpture are represented by unique reconstructions of wood-panelled rooms from houses in Kozani, Siatista and Hydra, as well as by numerous chests, island furnishings and a 19th century loom from Crete.

Rare ceramic pieces demonstrate the unbroken tradition of pottery-making stemming from the Byzantine period.

Outstanding examples of the weaver's work from Crete, Cyprus and Melos are included in the collection of woven textiles. In addition, almost every part of the Greek world is represented by embroideries dating from the 17th and 18th century, among which are remarkable examples of needlework from Epirus and the Ionian Islands, bed clothes from Asia Minor, embroideries from Skyros and Cyprus, and a magnificent bridal bed-canopy from Rhodes.

In addition to isolated fragments such as tunics from Karpathos and a pleated and embroidered skirt from Crete, the collection of Greek costumes includes complete outfits from many different regions.

The Museum also possesses an exceptional collection of jewellery from northern and central Greece, Attica, the Dodecanese, the Cyclades, the Ionian Islands and Asia Minor. Of especial interest are the well-known three-masted caravels and the golden necklaces from Siphnos and Patmos, as well as the gold ear-drops from Kos.

Finally, the art of stone-carving is represented by examples of work from the Greek islands, such as the marble decorative elements from a mansion in Ios, a fragment of the architrave of a marble sanctuary screen from the Cyclades and carved skylights from the island of Tenos.