The institutions of the Cisalpine Republic were very similar to those of France. Its first constitution, adopted on 8 July 1797, was based on the French Constitution of 1795. (Mantua), Panaro (Modena), Crostolo (Reggio), Reno (Bologna), Basso Po (Ferrara), Rubicone (Forlì). The membership of the local directories was reduced to three, and the municipalities for communes between 3,000 and 10,000 inhabitants were disbanded.

Trouvé appointed the new Directory, which had stronger powers, and a new parliament composed of two councils: the Anziani ("Elders") and the Giuniori ("Juniors"). The first was composed of 40 elected members together with the former directors. The second had 80 members.

A new coup d'état, attempted by French general Guillaume Marie Anne Brune the next autumn, was disavowed by the French Directory on 17 Frimaire (7 December).

Treaty of alliance

Formally, the Cisalpine Republic was an independent state allied with France, but the treaty of alliance established the effective subalternity of the new republic to France. The French, in fact, had control over the local police and left an army consisting of 25,000 Frenchmen, financed by the Republic. The Cisalpines were also required to form another army of 35,000 of their own men to take part in French campaigns.

On 4 March 1798, the Directory presented this treaty to the Great Council for ratification. The council did not agree with the terms and delayed taking a decision, but in the end, the French general Berthier compelled acceptance by the members. The Elders, however, refused it from the very beginning, as the new state was unable to finance the requested institutions. Berthier threatened to impose a military government but was later replaced by General Brune. The latter, after replacing some Elders and Juniors, achieved the signing of the treaty on 8 June.

Relationship with Switzerland

Due to multiple attempts by the Cisalpine government to annex the Italian-speaking Swiss territories south of the Alps, relations with the Swiss Confederacy were strained.