Maclay opposed the nomination of James Madison to the presidency by the Democratic Republicans. He doubted how committed Madison was to the party, considering him a late convert, and backed George Clinton instead. Furthermore, Maclay was an opponent of the Embargo Act which had been passed during President Jefferson's second term. Despite the eventual repeal of the Embargo Act, Madison secured Pennsylvania's support and Maclay realized that he was out of step with his fellow party members and Pennsylvanians. Seeing no hope of reelection, he resigned from the Senate in 1809.