The strength of evidence used to convict Alouni has been debated by lawyers, journalists and political experts worldwide.
An initial appeal against his sentence was rejected in January this year.
However, Spanish authorities decided last month that Alouni could serve the rest of his sentence under house arrest because of his deteriorating health.
True extent of disruption
Alouni, 50, is one of Al Jazeera's most well-known reporters. During the US-led invasion of Afghanistan, his reports revealed the true extent of disruption caused by bombings.
He was also Al Jazeera's bureau chief in Baghdad during the US-led invasion of Iraq. However, he left for his home in Spain when George Bush, the US president, said in May 2003 that the war was over.
In September that year, he was arrested at his home in Granada on the charge of "belonging to an al-Qaeda cell in Spain". This charge later disappeared.
The trial took place in spring and early summer last year. The verdict was announced only on September 26 - Alouni had been re-arrested 10 days earlier.
Lamis Andoni, an Al Jazeera journalist who had worked in Madrid with Alouni, said: "The arrest was a surprise since he was supposed to remain free until the ruling."
Baltasar Garzon, a supreme court judge in Spain, said that Alouni had helped structure al-Qaeda at "national and international level by financing, controlling and co-ordinating ... this criminal organisation".
The first piece of evidence used to justify this was that in 2000 Alouni had given $4,500 to a group of Syrians living in Afghanistan. These men were allegedly part of al-Qaeda.
However, the prosecutors could not prove that Alouni believed the recipients to be part of al-Qaeda.
Lack of evidence
The second piece of evidence used was Alouni's interview with Osama bin Laden after the attacks on the US of September 11, 2001.
During the court hearing, Pedro Rubira, a Spanish prosecutor, said to Alouni that "you look as though you were interviewing your boss".
Alouni had sometimes called bin Laden "sheikh" during his interview – an address used in Arab culture out of respect for the elderly or those of religious stature.
Joaquin Jimenez, a prominent judge in Spain, called for Alouni's acquittal because of the lack of evidence. He said the court had undermined Alouni's right to "presumption of evidence".
Quest for justice
He said the court had construed "evidence" and events in a post-9/11 understanding.
Andoni said the Osama bin Laden interview "was used as a catalyst to explain the facts, the events, so-called evidence which he [Jimenez] said was illegally collected to prove that Alouni has special links to al-Qaeda".
Despite his initial appeal being rejected, Alouni's lawyers never gave up the fight for justice and continue to work on his behalf.
And Andoni said: "Al Jazeera will support Taysir all the way in his quest for justice. We will support him appealing to the European Court of Human Rights in Strasbourg if he does not attain justice in Spain."