Succeeding Adams as president, Thomas Jefferson refused to continue paying Tripolitania the tributes stipulated by this treaty, partially leading to the First Barbary War.

[5] For three centuries up to the time of the treaty, the Mediterranean Sea lanes had been preyed on by the North African Muslim states of the Barbary Coast (Tripoli, Algiers, Morocco, and Tunis) through privateering (government-sanctioned piracy).

During the Revolution, the Kingdom of France formed an alliance with the former British colonies in 1778, now the proclaimed independent United States of America and assumed the responsibility of providing protection of U.S. merchant ships in the Mediterranean and eastern Atlantic Ocean against the Barbary pirates with the French Navy.

[6] After the Revolutionary War ended and the new United States won its independence with the signing of the Treaty of Paris (1783), it had to face the threat of the Barbary pirates on its own.

Commissioner Plenipotentiary (and Minister to the Kingdom of Spain in Madrid) of the United States, David Humphreys, was given the right to establish a treaty with Tripoli and assigned Joel Barlow and Joseph Donaldson to broker it.

The first U.S. president, George Washington, appointed his old colleague David Humphreys as Commissioner Plenipotentiary on March 30, 1795, in order to negotiate a treaty with the Barbary powers.

"[12] The treaty had spent seven months traveling from Tripoli to Algiers to Portugal and, finally westward across the North Atlantic Ocean, to the United States, and had been signed by officials at each stop along the way.

As Barlow declared: "The present writing done by our hand and delivered to the American Captain O'Brien makes known that he has delivered to us forty thousand Spanish dollars,-thirteen watches of gold, silver & pinsbach,-five rings, of which three of diamonds, one of saphire and one with a watch in it, One hundred & forty piques of cloth, and four caftans of brocade,-and these on account of the peace concluded with the Americans.

"[1] However, this was an incomplete amount of goods stipulated under the treaty (according to the Pasha of Tripoli) and an additional $18,000 had to be paid by the American Consul James Leander Cathcart at his arrival on April 10, 1799.

In Treaties and Other International Acts of the United States of America by David Hunter Miller, which is regarded as an authoritative collection of international agreements of the United States between 1776 and 1937,[15] Hunter Miller describes, "While the original ratification remained in the hands of Cathcart ... it is possible that a copy thereof was delivered upon the settlement of April 10, 1799, and further possible that there was something almost in the nature of an exchange of ratifications of the treaty on or about April 10, 1799, the day of the agreed settlement.

"[14] It is then that the Pasha declares in a Letter to John Adams on April 15, 1799, "Whereby we have consummated the Peace which shall, on our side, be inviolate, provided You are Willing to treat us as You do other Regencies, without any difference being made between Us.

As the Government of the United States of America is not, in any sense, founded on the Christian religion; as it has in itself no character of enmity against the laws, religion, or tranquility, of Mussulmen (Muslims); and as the said States never entered into any war or act of hostility against any Mahometan (Mohammedan) nation, it is declared by the parties that no pretext arising from religious opinions shall ever produce an interruption of the harmony existing between the two countries.According to Frank Lambert, Professor of History at Purdue University, the assurances in Article 11 were "intended to allay the fears of the Muslim state by insisting that religion would not govern how the treaty was interpreted and enforced.

Lambert writes, By their actions, the Founding Fathers made clear that their primary concern was religious freedom, not the advancement of a state religion.

He wrote to Secretary of the Treasury Oliver Wolcott Jr., September 26, 1800: "The Senate, my good friend, and I said so at the time, ought never to have ratified the treaty alluded to, with the declaration that 'the government of the United States, is not, in any sense, founded on the Christian religion.'

[24] To the dismay of many Americans, the new settlement included a ransom of $60,000 (equal to $1,220,800 today) paid for the release of prisoners from the USS Philadelphia and several U.S. merchant ships.