He joined the Executive Council under Charles Poulett Thomson (later Lord Sydenham) in 1840 as the Solicitor General. Upon the union of the two Canadas (1841) he was a member of its first executive council under Lord Sydenham, but soon resigned on the question of responsible government. In 1842 he formed an administration, in connection with Lafontaine, who suggested an equal partnership. Baldwin, however, refused and took the position of Deputy Premier under Lafontaine. He resigned the next year, after a quarrel with the Governor General, Sir Charles Metcalfe, on a question of patronage, in which he felt that of responsible government to be involved. At the general election which followed, the Governor General was sustained by a narrow majority, but in 1848 the Reformers were again returned to power, and he and Lafontaine formed their second administration on March 11 under Lord Elgin and carried numerous important reforms, including the freeing from sectarian control of the University of Toronto and the introduction into Upper Canada of an important municipal system.

Internal dissensions soon began to appear in the Reform party, and in 1851 Baldwin resigned. The special struggle leading to his resignation was an attempt to abolish the court of chancery of Upper Canada, whose constitution was due to a measure introduced by Baldwin in 1849. The attempt, though defeated, had been supported by a majority of the representatives from Upper Canada, and Baldwin's fastidious conscience took it as a vote of want confidence. A deeper reason was his inability to approve of the advanced views of the Radicals, or "Clear Grits," as they came to be called. On seeking re-election in York, he declined to give any pledge on the burning question of the Clergy Reserves and was defeated. In 1853 the Liberal - Conservative party, formed in 1854 by a coalition, attempted to bring him out as a candidate for the upper house, which was at this date elective, but though he had broken with the advanced reformers, he could not approve of the tactics of their opponents, and refused to stand. He died on the 9th of December 1858 in Spadina. Even those who most strongly opposed his measures admitted the purity and unselfishness of his motives. After the concession of responsible government, he devoted himself to bringing about a good understanding between the English and French speaking inhabitants of Canada, and his memory is held as dear among the French Canadians as in his native province of Ontario.

The Baldwin family was a prominent one. Robert Baldwin counted among his cousins such influential Upper Canadians as the Anglican bishop Maurice Scollard Baldwin, Toronto mayor Robert Baldwin Sullivan and the Irish - Catholic leader Connell James Baldwin. Robert Baldwin is the grandfather of Frederick Walker Baldwin a distinguished Canadian engineer, politician, and football player who worked with Alexander Graham Bell. Robert Baldwin is also the grandfather of Robert Baldwin Ross a Canadian literary figure and confidante of Oscar Wilde.

Robert Baldwin, Esquire, Barrister, of York (now Toronto) married Augusta Elizabeth Sullivan, daughter of Daniel Sullivan, on May 3, 1827. The couple had four children, two sons and two daughters. Augusta Elizabeth died in January, 1836 and Robert Baldwin died in December, 1858.