A Democratic-Republican, he most notably served as Thomas Jefferson's first attorney general, and played a significant role in the events that led to the celebrated Marbury v. Madison court case.

He entered national politics with his election to the United States House of Representatives in 1800, but was immediately tapped by Jefferson to become Attorney General.

He served on a commission that resolved claims emanating from the Yazoo land scandal in Georgia, and advised Jefferson on matters related to the Louisiana Purchase.

In addition to distributing federal patronage dollars, he frequently reported to Jefferson on political sentiment in New England, and advocated for Republican positions in the newspapers.

In 1801, he founded the National Aegis, a newspaper dedicated to advancing Republican arguments and countering Federalist positions printed in other Massachusetts publications.

[15] Lincoln was regularly the subject of unflattering partisan newspaper reporting, as well as sermons delivered by influential Congregational ministers.

The negative sermonizing prompted Lincoln to publish a pamphlet entitled Letters to the People, by a Farmer in 1802, in which he lambasted the Federalists for politicizing the clergy.

Reverend William Bentley observed that Lincoln's criticism was a serious blow: "[N]ever did the Clergy suffer a more serious diminution of their influence and of their power.

[17] During this time, Lincoln was involved in actions that led to the celebrated Marbury v. Madison case concerning judicial review.

Some intended recipients of the commissions, William Marbury among them, filed a suit in the United States Supreme Court to compel their delivery.

By the time Jefferson assumed office, the United States Navy had been developed to the point where it might adequately defend American shipping interests.

Jefferson consequently refused to pay tribute in 1801 to Yusuf Karamanli, the ruler of Tripoli, after which the Tripolitans began attacking and seizing American merchant vessels.

Lincoln pointed out that only Congress had the authority to declare war, but the rest of the cabinet was intent on taking some sort of action.

[24] To circumvent these concerns, Lincoln made a novel proposal that the territory could be acquired by expanding an existing state's borders, effecting a purchase that would not require a constitutional amendment.

Federalists seized on the divisions in the opposition, claiming that Sullivan was a pawn, and that he would soon be replaced by the "Jacobin Lincoln—a man so little known, and so unpopular where known, that they dare not risk as a candidate for the office he aspires to.

From these positions, he continued to actively support the policies of President Jefferson, despite their growing unpopularity with the generally Federalist Massachusetts population and business interests.

[29] Lincoln ran for election as governor in his own right in 1809, but he was perceived by moderate Federalists as overly partisan and lacked the charisma of Sullivan.

[30] His support for Jefferson's economic policy, particularly that of embargoing trade with Great Britain and France (who were then embroiled in the Napoleonic Wars) was costly.

In 1811, President James Madison offered him a position as an Associate Justice of the Supreme Court, but he declined on account of failing eyesight.

His original burial site is not documented in the family genealogy, but he was eventually reinterred at Worcester Rural Cemetery after its establishment in 1838.