When the royal family had to flee to Brazil (in 1807), following the invasion of Portugal by French troops, the work proceeded very slowly with Fabri taking charge of the project, later followed by António Francisco Rosa.

[1] When the palace finally became a permanent residence of the royal family during the reign of Luís I and his wife, Maria Pia of Savoy, their architect, Possidónio da Silva, introduced many aesthetic changes and turned one of the lateral façades into the main one.

Perturbed by the events, King Joseph refused to live under a residence of masonry,[2] and took refuge in a wooden cabin next to the Palace of the Counts of Óbidos (packed with tapestries from the Quinta de Baixo).

[2][3] Since his successor, Queen Maria I of Portugal lived with Peter III in the Palace of Queluz at the time of Joseph's death, the Royal Barraca was vacated.

But, Manuel Caetano de Sousa designed an overcomplicated and intricate Baroque building (which was later criticized by da Costa e Silva and Fabri in 1801).

By 1807, the painters, sculptors and decorators had been contracted, but the arrival of Jean-Andoche Junot's forces immediately stopped the build as the royal family fled to Brazil (Rio de Janeiro).

In 1814 and 1815 work progressed in the rooms and staircases that were completed, with Taborda, Fuschini, Calisto, Cirilo Volkmar Machado (and his assistant Oliveira Góis), and Máximo Paulino dos Reis as painters, while decorator Manuel Piolti took over the interior layout.

Several individual projects were completed in 1818: Domingos Sequeira returned to direct the painting of the palace; the model for the south tower, authored by José Joaquim de Sousa was completed; on 26 September the vaulted ceiling was erected in the vestibule; and on 12 November, the decorative works in the Sala dos Embaixadores (Ambassador's Hall) were cleaned by contractors Severiano Henrique Pereira and Francisco de Paula.

King John VI, still in Brazil, began to show interest in the project, and presented the designs to his local architects Auguste-Henri-Victor Grandjean de Montigny and João da Silva Moniz.

On 15 February, in the Sala dos Archeiros (Archer's Hall), the painters Vicente Paulo Rocha and João de Deus Moreira, painted the base boards, following the designs of Manuel Piolti (since José Francisco Ferreira quit the project).

By May, Volkmar Machado proposed a new eastern façade, with a triangular apex and allegorical sculptures, alluding to the expulsion of the French during the Peninsular War, but the project was dropped.

Between 1819 and 1920, sculptures of Justice and Prudence were completed by de Aguiar; the ceilings of the Archer's Hall and Cane Concierge's Hall by Taborda (1766–1836) were completed, its doors first started by Piolti (1770–1823); the metal shields on the doors were provided by the Army arsenal; the ceiling of the Hall of Spanish Tapestries by Volkmar Machado, with perspectives by Piolti, figures by Joaquim Gregório da Silva Rato and ornamentation by André Monteiro da Cruz; skirting by bronzer and gilder Pierre-Philippe Thomire (1751–1843); the ceiling of the antechamber of the Sala do Despacho (Order Room) was completed by da Cruz and Taborda.

[1][2] It was proposed to the architects that the project's scale be reduced, encompassing only one-third of the original design, making the eastern façade the main entrance and erecting a tower at the southern end.

[2][3] The move of the Royal Court to Queluz Palace in 1829, and the death of the architect Rosa, resulted in a slowing of the project, and the affected the north wing which fell into ruin.

[2][3] With the restored Liberal regime, Peter IV took over as Regent until his daughter's age of majority, swearing allegiance to the Constitutional Charter in the throne room on 30 August 1834.

[2] After being acclaimed king (22 December 1861), Luís moved temporarily with to the Palace of Paço de Arcos, while remodelling occurred at Ajuda to adapt the building to become the new royal residence.

[2][3] In order to become liveable, the King directed Possidónio da Silva and Costa Sequeira to renovate and remodel the building, primarily based on the tastes of the Queen.

In the office adjacent to the Winter Garden, the walls were lined in pink velvet to house a collection from Saxony and the ceiling stucco was painted with representations of birds and views of Italy and Lisbon, by Giuseppe Cinatti and Achille Rambois, while the furniture was selected by Krieger, Suc.

Renovations also proceeded in the palace chapel, Queen's washroom and dining room by Leandro Braga, who was also assisted by Atelier responsible for the King's painting studio and personal library.

Other additions to the palace followed in subsequent years: in 1863, a bust of Maria Pia was executed by Santo Varni; an inlaid table was completed by Focentino Eugenio Azgnani (a wedding gift to Maria Pia, from the city of Faenza); in 1865, the execution of the sculpture by Odoardo Fantacchiotti (1809–1877); Maria Pia solicited Possidónio da Silva to substitute the painting in the ceiling of the Sala de Música (Music Room), the allegorical scene painted by José da Cunha Taborda and Arcangelo Fuschini, was substituted by one commissioned by Felisberto António Botelho; the Sala Azul (Blue Room) was lined in silk; in 1866, a marble statue, Tangedoura do Pandeirowas completed by Giovanni Dupré (1817–1882); in 1867, the parquet floor in the Sala do Despacho and Sala dos Contadores was completed by Godefroy, a joiner in the Belgian Royal House; the execution of the sculpture Mulher com bilha à cabeça by Célestin Anatole Calmels; the execution of a bust of King Luís I, also by Anatole Calmels; in 1869, the execution of the sculpture Leda by Cesare Sighinolfi; a painting of the King was also completed by the painter António Rodrigues da Silva; in 1870, Maria Pia mascarada by Joseph Layraud; in 1873, work on the parquet floor in the Sala Azul (Blue Room) by Joseph Godefroy; in 1874, paintings of the Princes Carlos and Afonso in the Sala Rosa (Pink Room) were completed by Joseph Layraud.

[3] By the end of the 19th century, new exterior restorations had begun, under the direction of Domingos Parente da Silva, while new additions continued within the interior: in 1875, a sculpture of Maria Pia was completed by Cesare Sighinolfi; in 1876, a painting in miniature of Luís and Maria Pia by Michele Gordigiani; in 1879, a new parquet floor in the Sala do Archeiros (Archer's Hall) and the Sala do Porteiro da Cana by Mardel Magalhães was begun; a painting of a canvas representing Umberto I of Italy by A. Jangiovanni was also installed in the same year; in 1881, the sculpture O Saltimbanco by Simões de Almeida was executed; in 1886, the a sculpture of Victor Emmanuel II, by Joaquim Santos; in 1887, paintings over the doors of the Queen's vanity by Ernesto Condeixa; in 1890, the portrait of Infante Carlos for the ante-chamber of the Sala do Despacho was completed by José Malhoa; in 1891, a new marble floor for the Sala dos Embaixadores (Ambassador's Hall) commission by António Moreira Rato & sons was installed; After the death of her husband, Queen Maria Pia continued to live in the palace with her son, the Infante Afonso.

[2][3] Although King Carlos of Portugal began to reside in the Palace of Necessidades, the palace (although residence of the Queen Mother) was reserved for official ceremonies, including banquets and receptions, such as those in honour of Edward VII of the United Kingdom of Great Britain and Ireland, Alfonso XIII of Spain, Wilhelm II, German Emperor and President Emile Loubet of France.

[2][3] Carlos made few changes to the palace, although he was responsible for ordering two large pots in Berlin from the Parisian factory of the Duke d'Angoulême, for the Sala do Trono (Throne Room).

Manuel II remained in residence at the Palace of Necessidades following the death of the King and Crown Prince in the Lisbon Regicide, during the tumultuous years before the revolution.

The Serviços dos Monumentos Nacionais (National Monument Services) branch examined the building to determine its condition (in 1956), which also predicted a large investment to completely restore the palace.

After a period of restricted access (between 1940 and 1968), when only people who had an authorization card from the Direcção Geral da Fazenda Pública (General Directorate of the Treasury), the palace was opened to the public on 20 August 1968.

[2] In 1989, the president of the IPPC, invited civil engineer Garcia Lamas and architect Gonçalo Byrne to elaborate a project to finish the palace.

The uncompleted western façade show signs of vestiges of various dependencies with a wall of open window sills/arches with Tuscan pillars and access to the central courtyard by three rounded arches.