In 1783 four “Philosophical Expeditions” departed from Lisbon to Portuguese Overseas Territories – Brazil, Angola, Mozambique-Goa and the Cape Verde Islands – in order to explore and catalogue their untapped natural resources. They were led by four young naturalists, former students of Domingos Vandelli at the University of Coimbra. Numerous shipments of natural products of the flora and fauna were sent to the Royal Museum and Botanical Garden of Ajuda, including specimens, drawings, maps, and reports. In 1808, during the French occupation of Portugal, the best specimens and manuscripts from the Museum of Ajuda were expropriated by Étienne Geoffroy Saint-Hilaire for the Muséum national d’Histoire naturelle in Paris. Since then, no systematic review has been conducted with these collections, except for the botanical material from Cape Verde. In order to accomplish the goals of analysing and identifying the botanical outcomes of those Portuguese scientific expeditions, the following materials were investigated: 1) herbarium specimens from the “Herbarium Brasiliense Dr. Alexandre Rodrigues Ferreira”, deposited in the Herbarium of the National Museum of Natural History and Science (MUHNAC) of the University of Lisbon (LISU); 2) those from the “Herbarium Lusitanicum”, which were taken by Geoffroy Saint-Hilaire to the Paris Herbarium (P); 3) the duplicates/unicates (ex LISU) that were sent in 1874 to the Royal Botanic Gardens, Kew (K); 4) the original iconography produced by the draughtsmen José Joaquim Freire and Joaquim José Codina, currently preserved in the Manuscripts Section of the Fundação Biblioteca Nacional in Rio de Janeiro and in the Museums of the University of Lisbon; 5) copies of the original iconography, made by draughtsmen and disciples of the Casa do Risco of the Royal Museum and Botanical Garden of Ajuda, currently deposited in the Library of the National Museum of Rio de Janeiro; 6) memoranda and lists of shipments of material from the Philosophical Expeditions, which are found in the Manuscripts Section of the National Library of Rio de Janeiro and in the Historical Archive of the Museums of the University of Lisbon; and 7) the literature produced about Alexandre Rodrigues Ferreira and other Portuguese Philosophical Expeditions of the 18th Century to Angola, Cape Verde, Mozambique, and Goa. The official documents of the French requisition of specimens from the Portuguese collections reported a number of 2,815 herbarium specimens: 1,360 from Brazil (1,114 – Alexandre Rodrigues Ferreira, 129 – Joaquim Vellozo de Miranda, 117 – José Mariano da Conceição Vellozo), 88 from Cochinchina (João de Loureiro), 216 from Angola (Joaquim José da Silva), 289 from Peru, 35 from Goa (Manuel Galvão da Silva), 562 from Cape Verde (João da Silva Feijó), 83 from Cape of Good Hope, and 182 from Uppsala. Up to the present, considering only the collections of the Philosophical Expeditions, 1,284 specimens of the so-called Herbarium Lusitanicum in Paris have been located, belonging to 870 species attributable to Ferreira. From the other expeditions, 151 specimens from Angola, 345 from Cape Verde, and 15 from Goa have also been located. Among the disastrous consequences of that requisition, there was a gradual decline of the Royal Museum of Ajuda. The herbarium itself remained at Ajuda until 1874, when it was transferred to the Escola Polytechnica. The recovered specimens are currently at LISU, pertaining to the “Herbarium Brasiliense Dr. Alexandre Rodrigues Ferreira”, which encompasses 1,275 specimens of 973 species (390 of the latter attributable to him). In the present account, a contextualisation and synthesis of knowledge about the Portuguese Philosophical Expeditions, particularly related to botany, is presented. All located specimens are listed and commented upon whenever showing relevant issues on provenance, identification, possible mixture of material, erroneous attribution, or other points of interest, like geographical distribution, nomenclatural types, and typifications. The identity of Laurus discolor Rich. has been unveiled, which has priority over Endlicheria sericea Nees. I here provide a new combination in Endlicheria: Endlicheria discolor comb. nov. (≡ Laurus discolor Rich.). The holotype specimen of Thylacanthus ferrugineus Tul., collected in Angola by Joaquim José da Silva, is illustrated and confirmed to belong to Julbernardia paniculata (Benth.) Troupin. As Thylacanthus has nomenclatural priority over Julbernardia Pellegr., I here propose nine nomenclatural combinations in Thylacanthus: Thylacanthus bifoliolatus comb. nov. (≡ Paraberlinia bifoliolata Pellegr.); Thylacanthus brieyi comb. nov. (≡ Berlinia brieyi De Wild.); Thylacanthus globiflorus comb. nov. (≡ Brachystegia globiflora Benth.); Thylacanthus gossweileri comb. nov. (≡ Berlinia paniculata var. gossweileri Baker f.); Thylacanthus hochreutineri comb. nov. (≡ Julbernardia hochreutineri Pellegr.); Thylacanthus letouzeyi comb. nov. (≡ Julbernardia letouzeyi Villiers); Thylacanthus magnistipulatus comb. nov. (≡ Berlinia magnistipulata Harms); Thylacanthus seretii comb. nov. (≡ Berlinia seretii De Wild.); and Thylacanthus unijugatus comb. nov. (≡ Julbernardia unijugata J.Léonard). Additionally, lectotypes for the names Paraberlinia bifoliolata (second-step), Berlinia brieyi, Brachystegia globiflora, Julbernardia hochreutineri (second-step), Julbernardia letouzeyi (second-step), and Berlinia magnistipulata, as well as for Laurus discolor, are designated.