During his second term at the Ministry of Justice, he developed a notable reformist program that included revisions to the Bankruptcy Code, policies on judicial assistance and reforms to medical-legal services.

His departure from the government was one of the reasons for the disintegration of the Partido Progressista; accompanied by other important and/or prestigious figures he formed a new faction, Progressive Dissidence, with principles that were soon closely allied to the republican cause.

Alpoim was monarchist with poor conviction, and observed attentively the activities of the republicans in the press, commissions and made it clear his political alignments.

Accompanied by the Viscount of Ribeira Brava, he held meetings with Afonso Costa, then leader of the Partido Republicano (English: Republican Party).

By June, he had met with João Chagas and, later, at his home he hosted a small group of disenchanted politicians and dissidents that included Rui Ramos, the republicans Afonso Costa and Alexandre Braga, a couple of military officers, the Viscount of Ribeira Brava and physician Egas Moniz (who would eventually win the Nobel Prize), as well as a few Regenerator politicians.

João Chagas, who would become Prime Minister during the First Republic, noted: During the attempted Municipal Library Elevator Coup on January 28, 1908, he took refuge at the home of the Regenerator politician António Teixeira de Sousa, before escaping into exile in Salamanca.