The Muslim cleric, who supports the implementation of Sharia Law in the UK, was attending worship at the London Central Mosque where around 100 members of far-right groups Britain First and the English Defence League chanted and waved banners against Islam.
The protesters were had to be held back by police as they campaigned against Choudary and clashed with Muslims attending afternoon prayers. Some tweeters reported that the right-wing movements were objecting to a planned protest by Choudary himself.
Speaking outside after prayers, Choudary told Muslims not to vote at the forthcoming election.
He also handed out leaflets entitled "why it is strictly forbidden to vote in Islam". One passage read: "Only God can make things lawful and unlawful. If a human being does this ... this is considered the most heinous crime."
However, he was accused by some worshippers of encouraging anti-Islamic protests.
The Britain First and EDL supporters shouted outside the mosque and the Islamic Cultural Centre, as hundreds of men, women and children moved inside for prayers, and had to be held back by police.
Some of the EDL and Britain First protesters chanted anti-Islamic messages, while others held up placards.
Just passing the Regent's Park Mosque, and it is HEAVING with police and racist EDL protesters. Bonkers. pic.twitter.com/bad7ZiYDMP— Adriana (@ASmallTurnip) April 3, 2015
Around 100 police kept them away from the front of the mosque, although trouble threatened to escalate when a handful of far-right demonstrators surged down the pavement towards a group of Muslims.
The protesters, who said they were antagonised by some of the worshippers, had to be restrained by officers.
Members of the EDL sang "It's our country, we're taking it back" to the tune of the Beach Boys' Sloop John B as prayers were being held, while others simply shouted "Scum".
Choudary formed banned Islamist group Al-Muhajiroun and has been accused by The Washington Post of "preaching for the Islamic State on the streets of London".
He was arrested last year in connection with being involved with groups that support terrorism.
Symbiotic relationship between Far Right & Islamist fringe:— Ben Quinn (@BenQuinn75) April 3, 2015
Britain First preparing to oppose Anjem Choudary protest pic.twitter.com/NfMxU1SkI3