The collection of Portuguese art reflects in a harmonious manner, a chronological route of the works ordered for the churches and chapels of the Funchal Diocese. In this museum are also integrated works attributed foreign artists, mainly Iberians, who worked in Portugal, as well as art of the meeting of cultures.
Thus, we see works of art from the 15th to mid-18th centuries.
In the goldsmithery, besides pieces coming from many churches all over the island, special importance is given to the set that makes up the so-called treasure of the Cathedral, which, in its majority, is deposited in the museum.
Among the pieces that go back furthest in time, there is the brass Processional Cross from the mid-15th century, as well as the Processional Cross of the parish church of Gaula, made of silver with traces of gilding from the late 15th century and early 16th century.
Particularly notable as a major work of Portuguese Manueline goldsmithery is the Processional Cross of the Cathedral, a gift from D. Manuel I, as well as an osculatory, with a Renaissance outline, and an aspersorium which bears the armillary sphere, the royal symbol, on the inside. In the set of royal gifts, there is also a Doorkeeper's Mace.

The Museum has an important collection of Mannerist goldsmithery, with works that can be dated from between the second half of the 15th century and the mid-17th century. This set of works of particular richness, due to its diversity of form, reveals a Portuguese taste that is permeable to the novelty of Spanish and Flemish plateresque. This includes trays, Eucharist vessels and aspersoria of special quality. This set is a partial representation of the extraordinary set of plain goldsmithery found on the island of Madeira, with special notice given to the sets of the Parish Church of Ribeira Brava, or the lesser known one of the Parish Church of Calheta.
A separate reference should be made for the group of incense boats, coming from various churches, with special attention given to the incense boat of Câmara de Lobos, dated 1589.
The silver amphora of the Cathedral is from the mid-17th century, as is the Salver of the Misericórdia of Funchal.
The collection of 18th-century goldsmithery is also greatly varied in its types and artistic quality. Examples are the chiselled and relief silver Urn by a Lisbon workshop, from the Funchal Cathedral, and the chiselled and cut-out silver bell from a Lisbon workshop of the middle of the century. A special note should be given to an Aspersorium and Sprinkler by the Madeiran goldsmith João Jacinto Teixeira (1775-1810).
Also notable is the gold monstrance of the Funchal Cathedral dated 1799, made by the goldsmith Paul Mallet, who worked in Lisbon.

In sculptures it is also possible to organise a chronological path between the mid-16th century and the end of the 18th century.
The recent discovery of a St. Sebastian from the early 16th century in stone from Ançã, attributed to Diogo Pires, o Moço, was important. Special reference should also be given to the set of sculptures, a part of which is on exhibition, from the old dressing room of the Cathedral, attributed to Manuel Pereira around 1648, with the works in low relief of Charity, Abraham and Melchizedek, The Ark of the Covenant, Agnus Dei, and the Vision and Calling of Isaiah, Pelican feeding its young, Abraham and the Angels, St. John and Christ at the Supper, Phoenix in Flames. In the set, there is also a Last Supper, with half-figure sculptures, gessoed, polychrome and gilded.
From the mid-17th century there is also an Our Lady of Light, from the altar of the same name in the Church of St. John the Evangelist of the Colégio in Funchal, as well as Our Lady of the Conception from the Church of Bom Jesus da Ribeira, which according to the inscription on the base was blessed by D. António Teles da Silva, Bishop of Funchal (1675-82). Also to be noted is the sculpture by a Portuguese workshop of the mid-17th century, of St. Isabel, Queen of Portugal, originally in the Convent of the Incarnation, in Funchal.
In the religious sculpture of the 18th century, we point out the image of St. Francis of Paula, the Archangels Raphael, Michael and Gabriel, presented in shrines of the era, from the Carmo Church in Funchal and the Cathedral, or Our Lady of the Angels from the Carmo Church and Our Lady of the Remedies and of Help, similar to those from the atelier of Machado de Castro, deposited in the Museum by the heirs of Dr. Rui da Câmara and coming from the Chapel of the Quinta de São João in Funchal.

In the collection of Portuguese paintings, without the unity found in the Flemish set of paintings, there are some works of quality on display, such as the painting from the Cathedral of St. Boaventura(?) of the late 15th century, which entered the Museum collections recently. Ecce Homo is from the mid-16th century and originally was in the old convent of Our Lady of Mercies. There is also a painting of The Ascension of Christ, attributed to Fernão Gomes and dated from the last decade of the 16th century. The paintings of St. Benedict and St. Vincent are also of interest, probably being found originally in the Chapel of St. Sebastian in Funchal, and attributed to Francisco Venegar, from the last quarter of the 16th century. Another painting in the Museum that merits mention is the Eleven Thousand Virgins, by Martim Conrado, and dated 1653.