He was subsequently elected to the Argentine Chamber of Deputies on the Autonomist Party ticket, as a close ally of the new Governor of Buenos Aires Province, Adolfo Alsina.

[1] Permitted to hold multiple posts outside Congress, Alcorta was later appointed prosecutor and judge, as well as to the board of directors of the Buenos Aires Western Railway.

He served Governor Alsina as Minister of Government Policy, of Economy and as President of the Bank of the Province of Buenos Aires.

His January 1895 reappointment to the Foreign Ministry by President Luis Sáenz Peña coincided with difficult negotiations with the Government of Chile regarding the Andes-range border shared by the two nations.

His second turn at the Foreign Ministry was devoted to the resolution of the Puna de Atacama dispute between the two nations, negotiations on which resulted in an 1898 treaty favorable to Argentina.