Le Pen on Tuesday morning refused to enter Sunni-Muslim Grand Mufti Andellatif Deriane's office, telling reporters "I will not cover myself up".
She had not cancelled the appointment when told on Monday that she was expected to wear cover.
Pointing out that she had met the Grand Mufti of Egypt's Al Azhar mosque, she commented, "The highest Sunni authority in the work did not insist on this."
No access to president's office
With President Michel Aoun being the first foreign head of state to agree to meet her, Le Pen hoped that the visit would improve her credibility as a player on the world stage.
But Aoun, a Christian who holds the presidency thanks to a constitutional power-sharing arrangement between confessional groups, met her in a large, impersonal reception room, while he had met centrist French presidential candidate Emmanuel Macron in his own office.
Officials stressed that the president was ready to meet all the candidates.
The Al-Akhbar paper, which supports Aoun's allies in the Shia-Muslim Hizbullah movement, published a front page telling the National Front (FN) leader "You're really not welcome in Beirut".
And, when Le Pen placed a wreath "in memory of French soldiers who have died for France in Lebanon since 1975" in front of the French ambassador's residence, no embassy representative was there to greet her.
Disagreements over Syria
Le Pen was obliged to note "differences in analysis" of the Syrian conflict after meeting Prime Minister Saad Hariri.
The only "viable and plausible solution" was to support Assad, she told him, a message that is unlikely to have gone down well, since Hariri holds Assad's regime responsible for the bomb that killed his father Rafic in 2005 and heads a coalition formed to force Syrian troops out of Lebanon.
Assad is "obviously a much more comforting solution for France than the Islamic State", she told the media afterwards, insisting that Syria faces a "binary choice" between the present regime and the armed fundamentalists.
Hariri pointedly warned her against confusing Islam and terrorism.
"The Lebanese and the Arabs, like the majority of the world, consider France to be the fatherland of human rights and that the republican state makes no distinction between its citizens on ethnic, religious or class grounds," he said in a statement after their meeting.
Addressing the persecution of Christians by fundamentalists in the Middle East, Le Pen told Foreign Affairs Minister Gebran Bassil that the best way to defend them would be to "eradicate Islamic fundamentalism", so that they can "stay on their land".
And she hailed "courageous and generous Lebanon", whose population is four million, for taking in about one million Syrian refugees, some of the migrants the National Front believes should not be allowed into Europe.
Historic ties to right-wing Christians
The FN has longstanding links with right-wing Lebanese Christians, some of its members having gone to fight in the ranks of their militias during the 1975-1990 civil war.
Le Pen's father, Jean-Marie, whom she expelled from the party in 2015, managed to meet then-president Emil Lahud in 2002 and she told guests at a dinner in Byblos organised by far-right businessman Roger Eddé that she had heard so much about the country from him.
"No ties are closer than those forged by shed blood," she declared. "We have these ties, these ties of blood shed together. It is indissoluble."
During her visit Le Pen made no comment on Monday's raid on her party's headquarters by investigators looking into charges that she and other FN MEPs claimed money from the European parliament for members who were actually working for the party.