France published the constitution of the new republic on 20 Messidor (7 July), establishing the division of the territory into eleven departments: Adda (Lodi), Alpi Apuane (Massa), Crostolo (Reggio), Lario (Como), Montagna (Lecco), Olona (Milan), Panaro (Modena), Po (Cremona), Serio (Bergamo), Ticino (Pavia), and Verbano (Varese).

On 25 Brumaire (15 November), the full international recognition and legality of the new state was ratified by the law governing the final annexation of the conquered territories.

The Executive Directory of the French Republic, not content with employing its influence, and the victories of the Republican armies, to secure the political existence of the Cisalpine Republic, extends its care still further; and convinced that, if liberty be the first of blessings, the revolution which attends it is the greatest of evils, it has given to the Cisalpine people their peculiar Constitution, resulting from the wisdom of the most enlightened nation.

That this transition should experience no shock, nor be exposed to anarchy, the Executive Directory thought proper to nominate, for the present, the members of the government and the legislative body, so that the people should, after the lapse of one year, have the election to the vacant places, in conformity to the Constitution.

It belongs to the Cisalpine Republic to show to the world by its wisdom, its energy, and the good organization of its armies, that modern Italy is not degenerated, and is still worthy of liberty.

The departments numbered eleven again, now covering larger geographical areas: Olona (Milan), Alto Po (Cremona), Serio (Bergamo), Adda and Oglio (Morbegno), Mella (Brescia), Mincio[3] (Mantua), Panaro (Modena), Crostolo (Reggio), Reno (Bologna), Basso Po (Ferrara), Rubicone (Forlì).

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 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.

After the defeat of France at the Battle of Cassano in April 1799 during the War of the Second Coalition, the republic was occupied by General Suvorov's Russian and Austrian forces, which appointed a provisional administration led by the Imperial Commission of the Mantuan Count Luigi Cocastelli [it].

On 3 Vendémiaire, year IX (25 September), the powers of the Extraordinary Commission were concentrated in the hands of a more restricted Committee of Government, composed of three members: Giovan Battista Sommariva, Sigismondo Ruga and Francesco Visconti, reflecting the institution of the French Consulate.

On 21 Vendémiaire (13 October), owing to the refusal of the escaped King Charles Emmanuel IV of Sardinia to sign a treaty of peace settling the situation of the occupied Piedmont, Napoleon ordered the annexation of Novara to the republic, shifting its western border from the river Ticino to the River Sesia.

After the surrender of Austria and the signing of the Treaty of Lunéville on 9 February 1801, the territory of the republic was extended to the east as well, placing the frontier with the Holy Roman Empire on the River Adige without the exceptions agreed in Campo Formio.

On 23 Floreal (13 May), the territory of the republic was divided into 12 departments, adding Agogna (Novara), restoring Lario and abolishing Adda-e-Oglio.

Two days later, in a scene officially commemorated by Nicolas-André Monsiau, Bonaparte appeared in the Collège de la Trinité of Lyon, attended by Murat, Berthier, Louis Bonaparte, Hortense and Joséphine de Beauharnais, and heard the assembled notables proclaim the Italian Republic.