The monastery surrounding the church had fallen into disrepair after 200 years of constant use, so during the reign of Emperor Ferdinand62 in 1840 the monastery (but not the church) was torn down and rebuilt. As part of that project, architect Johann Höhne built Ferdinand’s Vault and the Tuscan Vault as part of the basement of the new structure. As part of the jubilee celebrating his 60 years on the throne in 1908, Emperor Franz Joseph142 had architect Cajo Perisic build another mausoleum chamber and a chapel to the east of Franz II57 and Ferdinand’s62 vaults. At the same time, new annexes for visitors were created on either side of the church.
By 1960 it was obvious from the deteriorating condition of the tombs that the environment of changing heat and humidity needed to be controlled if the historic sarcophagi were to be survive for future generations. The New Vault, north of the Tuscan, Ferdinand’s and Franz Joseph’s Vaults, was built by architect Karl Schwanzer, with metal doors by sculptor Rudolf Hoflehner. It added about 20% to the space of the crypt, and was used as part of a massive rearrangement of the tombs in the vaults. The original small vault had held, besides the tombs of the two founders, those of a dozen children and had been called the Angel’s Vault. Those were moved to open niches newly made in the front wall of Leopold’s Vault. Selected tombs from various other vaults were moved to the New Vault and grouped in themes such as Bishops, the direct ancestors of the last reigning emperor, and the immediate family of Archduke Karl122 the victor of Apern. Thirty seven other tombs, of some minors and minor members of the ruling family, were walled-up into four piers created in Ferdinand’s Vault. Thus about half of all the tombs were moved out of the original vaults to more orderly places as part of that great reorganization.
In 2003 another project made the crypt accessible to the handicapped, and opened previously unused doors so that the visitor route no longer requires the 100% backtracking that was necessary before. The entire crypt was also air conditioned to prevent deterioration of the tombs. The free-standing tombs are usually variations of either a flat-topped storage chest, or a tub with sloping sides and a convex lid of tapered decks. Ornamentation ranges from simple to elaborate.
Until far in the 1700s, the most common material for a sarcophagus here was a bronze-like alloy of tin, coated with shellac. The splendid tombs of the baroque and rococo eras are made of true bronze, a nobler and therefore more expensive material. Reforming Emperor Joseph II42 decreed simplified burial customs for the people, and introduced the use of lighter and cheaper copper into the Imperial Crypt, where it was then used into the 1800s. In the later 1800s a mixture of cast brass and bronze as well as silver-bronzed copper was adopted. Other metals were used only rarely, except for silver and gold plating on decorations. Only one sarcophagus, that of Emperor Franz Joseph,142 is made from stone instead of metal. Various techniques of metalworking were used: full casting for the sarcophagus; hollow casting for decorative sculpture; carving, engraving, and hammered relief for surface decoration. The parts for chests and covers are riveted together, ornaments and decorative figures are screwed on. The sculptor responsible for the most elaborate tombs is Balthasar Ferdinand Moll.
In order to guarantee the stability of the enormous display tombs, they have iron bracings and wood lining inside. This avoids both cave-ins and a buckling of the side walls from the weight of the cover. (The cover of the double tomb of Empress Maria Theresia56 and her husband,55 weighs approximately 1700 kg/3,800 lb!)

Within the outer case lays a wooden coffin that is wrapped in silk (black with gold trim for rulers, red with silver trim for others). The coffin usually has two locks, the key to one is kept by the Capuchin Guardian of the crypt, the other is kept in the Schatzkammer of the Hofburg palace in Vienna. Within the coffin, the body usually has had the organs removed as a necessary part of the embalming process for its display before the funeral. For about one-third of the bodies, the heart has been placed into a silver urn and sent elsewhere (usually the Herzgruft in the Augustinerkirche), and for some the intestines and other organs have been put into a copper urn and deposited in the Dukes Crypt in the catacombs of Vienna’s cathedral, the Stephansdom.
Over the centuries, constant humidity, variations in temperature, and the host of visitors had taken a great toll on the sarcophagi. Corrosion craters, holes and tears had developed. Layers of the horizontal surfaces had peeled, base plates had broken through, decorative fixtures had been broken or stolen by visitors, the cast metal absorbed too much humidity and puffed up, and heavy covers had caused some sidewalls to bend or cave.
The first major restoration effort was undertaken in 1852, but further work was needed by 1956 when the Gesellschaft zur Rettung der Kapuzinergruft (Association for Saving the Capuchin Crypt) came into being to inform the public of the problem, raise funds, and preserve and restore the tombs. It was first necessary to create additional space and to dehumidify the crypt. After completion of the New Vault in 1960 and the transfer of 26 tombs from the overflowing Tuscan Vault, the work of dehumidification could begin. Also, a workshop was created in the south end of the Tuscan Vault where highly-skilled artisans could work on selected tombs temporarily moved there for restoration.

In 2003 remodelling of the ground-level visitor facilities took place to create a new visitor entrance and make the crypt accessible to the handicapped. The visitor route was also changed so that visitors now see the tombs in historical sequence by entering at one end and leaving at the other, instead of both entering and leaving via a single stairway that is in the middle of the route. Most importantly, the entire crypt was air conditioned so that humidity can be controlled. The repair and conservation of the artistic work takes place in close cooperation with the monks, the Association, the Austrian Monument Office and the Vienna Old City Preservation Fund. In 1960, with the various vaults overcrowded, a major rearrangement project began which resulted in the construction of the Children's Columbarium and the New Vault. At the same time many bodies were moved to those new areas, others were moved from the Tuscan Vault and Ferdinand’s Vault and walled up into the corner piers of Ferdinand's Vault. In 2003, the Vaults were air-conditioned, more for the preservation of the tombs than the comfort of visitors.