While editor of the Today programme, Liddle wrote a column for The Guardian newspaper. On September 25, 2002, he titled his column 'Marching back to Labour': referring to a march organized by the Countryside Alliance in defence of fox hunting, Liddle wrote that readers may have forgotten why "you" voted Labour but would remember once they saw the people campaigning to save hunting.
The BBC considered that this breached his commitments as an editor and gave Liddle an ultimatum to either stop writing his column or resign: he resigned on 30 September 2002. With Kate Silverton he went on to present BBC2 political show Weekend, BBC4's The Talk Show. He also continued to write for The Guardian, wrote a critically acclaimed book of short stories entitled Too Beautiful for You, became a team captain on Call My Bluff and also took a job as Associate Editor at The Spectator. He now also writes a weekly column for The Sunday Times.
Liddle defended Andrew Gilligan in the media during the Hutton inquiry.
In The Trouble with Atheism, Liddle argued that atheists can be as dogmatic and intolerant as the adherents of religion. "History has shown us," he says, "that it’s not religion that’s the problem, but any system of thought that insists that one group of people are inviolably in the right, whereas the others are in the wrong and must somehow be punished." Liddle argues, for example, that eugenic policies are the logical consequence of dogmatic adherence to Darwinism.
On 21st May 2007 he presented an hour long documentary entitled Battle for the Holy Land: Love Thy Neighbour concerning the Israeli-Palestinian Conflict. In the documentary Liddle visited Bethlehem, Hebron and the Israeli settlement of Tekoa. Liddle sought to examine whether Israel was a true Liberal Democracy in light of its treatment of the Palestinians. In particular Liddle sought to examine the human side of the conflict.
In 2005, Liddle was criticised by the Muslim Council of Britain leader Sir Iqbal Sacranie when he said, "The one we didn't want to hear, is the most accurate: Sacranie and Mr Bunglawala don't like Jews. They are both unequivocal anti-semites", after they had suggested a Genocide memorial day was more appropriate than simply a Holocaust Memorial Day.
Mr Bunglawala responded by affirming that:
It was also alleged that Liddle ignored the following statement made by the MCB about Holocaust Memorial Day earlier in the year.
Liddle was heavily criticised by pro-Muslim groups following the broadcast of his Channel 4 documentary 'Immigration Is A Time Bomb' in 2005. Amongst the complaints were that Liddle allowed BNP leader Nick Griffin to speak "unchallenged when arguing for freedom of speech" and that Liddle "stated that Griffin should not have been arrested for stating his views" for incitement to racial hatred. Griffin was eventually cleared, in November 2006, of all charges relating to that arrest. He had already previously received a two year suspended sentence in 1998 for inciting racial hatred in a completely separate case.. Ofcom adjudicated that the programme was entirely fair, and the complaints were dismissed.
In February 2006 Liddle wrote an article in The Sunday Times ('Alas, I must defend the BNP') supporting BNP leader Nick Griffin's right to free speech, after Griffin had been arrested for inciting racial hatred.
Liddle married his long-term girlfriend and HTV reporter, Rachel Royce, in March 2004 in Malaysia. They had been living in Heytesbury, Wiltshire, and had two sons together. Six months later, Liddle moved in with Alicia Monckton, a twenty-two year old receptionist at The Spectator magazine whom he had been seeing for some years, and his wife divorced him. It transpired that he had cut his honeymoon short so that he could go to comfort Monckton, whose mother had died.
On 5 May2005 Liddle was arrested for common assault against his then pregnant girlfriend Alicia Monckton. He was held under domestic violence guidelines which allow police to question suspects without cooperation from victims. He later was given and accepted a police caution for the offence. Liddle was reported as having claimed to have accepted the caution as it was the quickest way for him to be released, stating that he "never touched Ms Monckton".