Especially during his second term, Jefferson had to contend with growing conflicts between the French and the British. Both sought an elite status of supreme power in Europe, and Jefferson tried to sidestep the conflict by remaining neutral, believing that aligning himself with either side would destroy the American progress he had been able to forge.

United States relations with Britain became increasingly tense following Napoleon's Berlin Decree, which forbade travel with Britain; Britain responded with Orders in Council, which initiated a blockade of French-controlled Europe. Jefferson decided to proclaim an embargo on all foreign trade, which actually did not have much effect on Britain's economy. This balance of maintaining peace with both world powers at the time was a tricky sea to navigate.

As pirates from North Africa increasingly raided supply ships in the Mediterranean, Jefferson felt compelled to increase safety in trading. He ultimately gave orders for American warships to confront the pirates, and this Naval push had initial success until the pirates were able to capture an American frigate. This continued to be a source of tension throughout Jefferson's presidency.

He likely had a fear of speaking in public, which would be even more difficult in the absence of modern technologies. His speaking disposition has been described as "weak," and he lamented that he could not orally deliver speeches as passionately as he could write them. His inaugural address is described as having such a low tone that few could hear it.

Jefferson also had to contend with the issue of slavery during his terms in office. South Carolina had reopened international slave trade, and Jefferson denounced the violations of human rights innate in doing so. He passed the Act Prohibiting the Importation of Slaves, but this act did not address the domestic slave trade, which was a growing issue of concern.

As a new country, Jefferson was tasked with leadership in complex issues which would define the ultimate direction of the United States, and he was therefore embedded in numerous international and domestic issues of policy.

Jefferson had many obstacles, both foreign and domestic.  One obstacle was the Federalist Party.  After Adams lost the 1800 election, many in the party thought that the United States would fall apart or at least undergo a violent civil war.  Jefferson had to deal with the Federalist judges put into power by exiting president John Adams.  Jefferson also had to deal with a partisan press that was willing to slander his name and other Democratic-Republicans.  Of course, Jefferson also had his own newspapermen who did the same thing to prominent Federalists.  

Internationally, Jefferson sent a naval force to defeat the Barbary pirates.  In retaliation for stopping ships at sea, Jefferson leveled the Embargo Act against Britain and France; this also killed American trade in Europe and only increased Federalist disapproval.  Jefferson also had to handle problems with Indians on the Western frontier who were being armed by the British.  

One of the greatest challenges to Thomas Jefferson’s presidency were the Federalists. After Jefferson and Burr won the elections, the Federalists tried to vote against Jefferson. However, abstention by some Federalists saw Jefferson assuming the well-deserved title of president.

As president, Thomas Jefferson attempted to reform the judiciary, but his attempts failed. Jefferson was interested in removing partisan judges from public office, but Federalist appointees to the judiciary and other Federalist members fought successfully against the plan.

In the Louisiana Purchase, Thomas Jefferson was forced to set aside his philosophy in order to secure the deal. He understood that the Constitution did not provide explicit procedures with regards to foreign territory, but the land was important for the greater good of the people. Some Federalists challenged the purchase based on the lack of constitutional provisions to make new land purchases. However, the President made his move, and the land was purchased. The purchase was approved by Congress five months later.

Thomas Jefferson faced several obstacles while he was president. One of those obstacles dealt with events at home.  Jefferson was a Democratic-Republican.  The courts had many judges who were Federalists, and they blocked many of his ideas.

Another issue dealt with our relationship with other countries. Britain and France were at war. Neither country wanted us to trade with the other.  Thus, both Britain and France interfered with our trade.  Jefferson tried a total stoppage of trade to keep our sailors and merchant ships safe. (Embargo Act of 1807)  However, our economy was very dependent on trade, causing this policy to fail.

Jefferson did stand up to the pirate countries of North Africa. We refused to pay them bribes so that they would leave our ships alone.  We fought them, and they stopped attacking our ships.

Jefferson had a moral conflict regarding the Louisiana Purchase. When Spain (and then France) wouldn’t let us use the port of New Orleans, Jefferson offered to buy this area from France.  When Napoleon offered the entire area of Louisiana, Jefferson wasn’t sure he could legally buy all of this land. He believed in a strict interpretation of the Constitution.  Nowhere in the Constitution did it say the president could buy land. Jefferson was persuaded to make the purchase!