Wadah Khanfar stood down after eight years that consolidated the satellite network's reputation and his own position

Seated behind a vast desk, surrounded by TV screens, deep leather sofas and a wall of global media awards, Wadah Khanfar always cut an impressive figure in his director-general's office at al-Jazeera headquarters in the Qatari capital, Doha.

But his career at the top of the most important news organisation in the Arab world ended on Tuesday when he was replaced by a member of the Qatari royal family. It was an abrupt and dramatic move at a critical time in the Middle East.

Khanfar, credited with revolutionising the Arab media landscape, said he was resigning after eight years that consolidated the satellite network's reputation and his own highly influential position.

The new boss is Sheikh Ahmed bin Jassim Al Thani, a little-known executive at Qatargas and a member of the fabulously wealthy Gulf country's ruling dynasty – pointing to a clear attempt to exercise greater control.

It is thought that Khanfar had become too independent a figure for the Qataris, and that he had come under pressure from them. Recently al-Jazeera has been accused of pulling its punches over the uprising in Bahrain, where Saudi Arabia dominates regional policy. Al-Jazeera's Lebanon chief, Ghassan Bin Jiddo, resigned in April, apparently in disagreement over coverage of some of the revolts.

But on Tuesday night Khanfar denied speculation that his departure was linked to outside pressure. He told the Guardian: "I have spent eight years with the network. We have been talking in this part of the world about change, about presidents who stay for decades in their posts. I thought maybe it is good to give an example as well, while the network is at the peak of its performance. It's the right moment."

The Palestinian-born journalist said his resignation had "nothing to do with any of the speculation" swirling on Twitter, and said he agreed "a couple of months ago" with al-Jazeera's board to step down.

Describing the channel's coverage this year as "amazing", he added: "We have stood with the people and supported their freedom. I maintained the independence of the network regardless of all the pressure we received. I think this will continue."

Al-Jazeera staff said Khanfar seemed emotional when he addressed them after announcing his resignation – but refused to divulge exactly why he had gone now. "People can think what they like," he told them.

"It's seismic," said one journalist on the AJ English channel. "We are all in shock. This was a guy who had had a meteoric rise and he was at the very top of his game."

Arab sources close to the Qatari government said the move had indeed been discreetly planned six months ago but had to be delayed after a leak from Syria suggesting Khanfar's removal was imminent – to avoid the impression of caving in to pressure from Damascus.

Al-Jazeera, owned by the emir, broke the mould of Arabic media organisations that were bankrolled by and subservient to governments when it was set up in 1996. Often technically brilliant and highly partisan, it has outperformed itself in this extraordinary year of Arab uprisings with the slogan – echoing the battle cry of past revolutionary struggles – that "the coverage continues".

Khanfar reflected the channel's sense of mission when he wrote: "In 2011 the eyes of the world watched the aspirations of millions unfold as our newsrooms broadcast, tweeted and published the events unfolding in the Liberation Squares from Sidi Bouzid [Tunisia] to Jisr al-Shughur [Syria]. The coverage of these revolutions is ongoing, and we continue to report the fight of the youth to achieve dignity and freedom from tyranny and dictatorship."

Confident, charming and articulate in English as well as his native Arabic, Khanfar is a high-profile figure on the international conference circuit. Khanfar's critics say his sympathy for the Muslim Brotherhood shows in often favourable coverage of Islamist movements.

But, talking to the Guardian, he rejected that criticism. Islamist groups played an important part in the uprisings and therefore featured, he said.

In Libya, for example - which he has been visiting this week - al-Jazeera has been giving air time to a prominent Islamist exile who had been in exile in Qatar. Khanfar also promised to give a platform to leaders of the opposition Syrian National Salvation Conference.

Not surprisingly, he has many enemies. The PLO was furious about the leak to Al-Jazeera of documents exposing embarrassing details of its secret negotiations with Israel.

In Jenin in the West Bank, the family home, Khanfar's brother is a Hamas activist. Reactions to his departure included the comment by one pro-regime Syrian that he had been "exposed as a CIA asset", a reference to WikiLeaks documents that show him meeting US diplomats in Doha.

Khanfar shrugged off these revelations, and the suggestion they had successfully persuaded him to moderate elements of the channel's coverage. "Our meetings with the US have to be put in context. I have meetings with presidents, meetings with foreign ministers, with representatives of the governments of China, the US, Britain, Sudan and other countries in the world."

"Always we receive complaints. If the complaint has any merit we deal with it. Sometimes we make mistakes. We accept it. But if it's political we don't actually take it into consideration."

Qatar's leading role in supporting the anti-Gaddafi rebellion in Libya has required the emir to build a broader Arab consensus. This has also seen him patch up once rocky relations with Jordan, which was accused last year of blocking AJ broadcasts of the World Cup from South Africa. Arab power-politics and editorial independence have clearly been in sometimes sharp conflict.

But as Blake Hounshell of Foreign Policy magazine put it: "Whatever you think of al-Jazeera's coverage, there's no question @khanfarw put the network on the global map. Big time." As'ad Abu Khalil, the acerbic author of the Angry Arab blog, called him "very smart and dynamic".

Khanfar's resignation letter was clearly written with a view to fixing his legacy as the man who made al-Jazeera: "Authoritarian regimes were terrified at the birth of this new institution and they quickly went on the offensive," he wrote.

"From trying to discredit our reportage and staff through disinformation to lodging official protests with the Qatari government. When this did not stop our reporting, they started harassing our correspondents, detaining our staff and closing our offices. The only way they could stop us was by jamming our satellite signal. Yet we remained steadfast in our editorial policy – in fact, each attempt to silence us further emboldened us and increased our resolve."

Asked what he was going to do now, he said: "I'm going to continue in the same spirit of al-Jazeera. I'm going to very soon announce something related to it, related to the media and the ethics and standards of the profession."