Under this Union of the two Canadas he worked with Robert Baldwin and Francis Hincks in the formation of a party of Upper and Lower Canadian liberal reformers; he and Baldwin formed a government in 1842 but resigned in 1843. In 1848 he was asked by Lord Elgin to form the first administration under the new policy of responsible government.
The Lafontaine-Baldwin government battled for the restoration of the French language (abolished with the Union Act) and the principles of responsible government and the double-majority in the voting of bills. While Baldwin was reforming Canada-West (Upper Canada), Lafontaine passed bills to abolish the tenure seigneurial (seigneurial system) and grant amnesty to the leaders of the rebellions in Lower Canada who had been exiled. The bill passed but it was not accepted by the loyalists of Canada East who protested violently and even burned down the Parliament in Montreal.