The chief judge threatened to order everybody out of the room if they did not quieten. He later adjourned the trial until March 12.
Al-Zeidi's legal team argues that the charges should be dropped and the 30-year-old TV journalist be freed.
Dhiya al-Saadi, one of the lawyers acting for al-Zeidi, said on Wednesday: "He [al-Zeidi] was optimistic and ready to stand in front of the court, as he believes what he did was fair.
"He is counting on his release because he did not try to kill former president Bush and was only expressing his opinion."
'Freedom of expression'
Khalid al-Izzi, another defence lawyer, said they would also argue that al-Zeidi's actions were "spontaneous" and "against the president of the state that occupies Iraq".
"We will demand a reduction in the charge which is that he was threatening the life of a visiting president with premeditation ... We will argue that Bush was not on a declared official visit between two sovereign countries," al-Izzi said.
"In fact, Bush was visiting an occupied country and al-Zeidi was trying to express his personal rejection [of] that occupation."
The shoes al-Zeidi threw at Bush will not be presented as evidence in court because they were destroyed after being cut and checked for possible explosives.
Bush ducked and narrowly avoided being hit by the shoes while speaking at a joint press conference in Baghdad with Nuri al-Maliki, the Iraqi prime minister, on December 14, 2008.
The Al-Baghdadia TV reporter also verbally insulted Bush, calling him "a dog".
Bush dismissed the incident at the time, joking that the shoes were a "size 10".