Due in part to his inexperience at managing the army and a lack of preparedness, the military failures in the early months of the War of 1812 were laid on his shoulders, leading to his resignation.

[1] He served with the Continental Army in the New York and New Jersey campaign, refusing a lieutenant colonel's commission offered by artillery chief Henry Knox.

[6] In 1777 Eustis was placed in command of a military hospital established at the former residence of Loyalist Beverley Robinson north of New York City, where he remained for the duration of the war.

During his successful campaign against Josiah Quincy,[11] Eustis was charged with either authoring, or being complicit in the production of, letters that formed a part of the 1783 Newburgh Conspiracy, a threatened uprising in the Continental Army.

[13] He demonstrated this by voting against President Thomas Jefferson's repeal of the Judiciary Act of 1801, a Federalist bill passed in the late days of the John Adams administration that had greatly expanded the number of seats on the federal bench.

[22] As tensions grew between the United States and Great Britain, Eustis made modest moves to improve military readiness, but did not otherwise distinguish himself or introduce other initiatives or proposals.

When the War of 1812 began, the army's logistics were in shambles, and it had no overall commander, forcing Eustis to make detailed decisions for nine military districts.

[20] Treasury Secretary Albert Gallatin wrote that there was "a total want of confidence" in Eustis that was felt "through every ramification of the public service.

"[23] Eustis tendered his resignation in December 1812, and Secretary of State James Monroe took over his duties until John Armstrong assumed the office on February 13, 1813.

[25] Madison believed the post to be important for sounding out conditions in Europe due to The Hague's historical use as a neutral ground for negotiations, and he instructed Eustis to track European diplomatic sentiment.

[29] Eustis was at a disadvantage due to his lack of French language skill, and was recalled in 1818 after the Dutch government reduced its American delegation head to a chargé d'affaires.

[32] Upon his return from Europe, Eustis purchased the mansion in Roxbury built by royal governor William Shirley in the 1750s (which is now known as the Shirley-Eustis House).

[36] Republicans presented Eustis as a moderate successor to Brooks who would be less partisan than Otis, and also highlighted his Revolutionary War experience.

[38] Eustis' victory in the election (combined with a Republican sweep of the legislature the following year) marked the effective end of the Federalist Party in Massachusetts.

Burr and Eustis exchanged letters on the most intimate subjects, recommending potential romantic partners to each other and sharing a taste for well-educated women.

[46] Eustis aided Burr on one occasion by helping him find accommodations for a young woman whose mother had been involved in an adulterous relationship with Alexander Hamilton; she was placed in a Boston-area boarding school.

[47] Eustis may have also been the subject of a teenage crush by Burr's daughter Theodosia, who shared intimate details of her life with him (including medical conditions emanating from a difficult pregnancy) well into adulthood.