After returning to his homeland, he wrote several "patriotic works", which were booklets designed to strengthen popular resistance against the French, Manifesto da Razão contra as usurpações francesas oferecido à Nação Portugueza , aos Soberanos e aos Povos [Manifesto on the Reason against French usurpations offered to the Portuguese Nation, Sovereigns and Peoples] (1808); Observações sobre os recentes acontecimentos das províncias de Entre Douro e Minho, e Trás - os -Montes [ Comments on recent events in the provinces of Entre Douro e Minho and Trás - os -Montes] (1809); and Reflexões sobre a invasão dos franceses em Portugal [ Reflections on the French invasion of Portugal] (1809), among other works. Some of these were translated in Spain, where they achieved some notoriety.

After the first invasion was repelled and the national sovereignty was re-established to a limited extent, the patriotism and loyalty shown by José Acúrsio das Neves were honoured and he was selected for several posts. On 27 August 1810 he was elected a corresponding member of the Royal Academy of Sciences in Lisbon. Later that year, he was appointed judge the Oporto Court of Appeal, a post he would combine with the functions of deputy and secretary of the Royal Board of Commerce, Agriculture, Factories and Navigation, as well as deputy of the Royal Silk Factory, the Free Water Works and the Liquidation Board of the now-defunct General Company of Commerce of Grão -Pará and Maranhão. In recognition of his commitment, he was awarded the Orders of Christ and Our Lady of the Conception. These appointments in the fields of economics were decisive in consolidating his economic and political thinking, which was why he began publishing his thoughts on Political Economy in 1814, which included a contribution of lessons and examples taken from history, which was another of his great literary passions.

His most important work in the historiographical circles is, of course, the História Geral da Invasão dos Franceses em Portugal e da Restauração deste Reino [General History of the French Invasion of Portugal and the Restoration of this Kingdom] (vols. I-V, 1810-1811), which is still today an essential reference in any bibliography available on the French Invasions, with reissues up to the present day (1984/2008). As in all of his writings, his patriotic inclinations and defence of national independence are clear and obvious: "Force often, but not always, dictated these speeches; however, whether it was force, fickleness of character, treachery or cowardice, the effects were always the same. It is only right that the timid should find a forgiving mother in their homeland — one who will forgive them for their weaknesses when they come to her in repentance. However, the insolence of those who cover their infamy or their cowardice with the pretence of doing good for their homeland, and even describe their crimes as services and declare these are virtues — is beyond the most basic decency! These virtues are indeed very common in the unfortunate century of the Napoleons and the Godoys , but they would have found their reward on the gallows in the centuries of the Epaminondas, the Aristides and the Brutes! Virtue never supports crimes. The true good of the homeland demands its sons that, instead of joining the murderers who are tearing it apart, they should bravely expose their chests to bullets in order to save it" ( História Geral da Invasão dos Franceses ... Reino, vol. III, 1811, pp. 13-14). The guiding lines set in this work, which was still highly controversial, showed a view of history with key concepts that called for a revolution against the decadence of Portugal, with a need to rescue the country through progress and the strengthening of convictions about the homeland. Boldly published during the French Invasions, this work denounced, from the author's point of view, the betrayals and collaborationism of many important individuals, which, given the proximity of these events and the fact that those individuals remained in government positions, led to fiery controversies, of which we highlight, among others, the quarrel with Lieutenant General and academic Francisco de Borja Garção Stockler (1759-1829), which dragged on for more than a decade, with the publication of denials and justifications from both sides.

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