He knew the decision would put him at odds with his superiors and potentially cost him his liberty.
But despite the consequences, he took a stand because he believed his faith precluded him from killing fellow Muslims.
The veteran soldier claimed the Iraq war was illegal because America's main justification for invading the country - to destroy alleged weapons stockpiles - had been discredited.
Webster, who is currently incarcerated in an American base in Germany after his conscientious objector (CO) application was turned down, now faces a further year in jail.
The former sergeant, who has since been stripped of his rank, is one of an increasing number of American soldiers who have applied for conscientious objector status since the start of the Iraq war.
According to the US army, since 2003 it has received 96 applications, 48 of which have been approved.
This is more than four and a half times as many as the army received in 2001 and in 2002.
But JE McNeil, executive director of the Washington-based Centre for Conscience and War, says the military vastly underestimates the true number of applications.
"Nobody knows the true figures but it is definitely in the hundreds," she told Aljazeera.net.
"The military doesn't count the number of CO applicants who are in the middle of the process which can take up to two years.
Abd Allah Webster has been
separated from his daughter
"And many CO applicants are subsequently discharged from the army for other reasons, so they don't appear on the statistics.
"Before September 11 our organisation would only get one or two calls a month from soldiers wanting help filling out CO forms.
"But after 9/11 we were getting one call a week, and since the start of the Iraq war we have been getting at least one or two calls a day," she said.
She added: "There are definitely soldiers out there who specifically object to the war in Iraq, although they would be willing to participate in other wars. They think that it is immoral and wrong."
The US army defines a CO as someone who, for religious reasons, is opposed to all wars. If it adjudicates in favour of CO status, the army exempts a person from combat training and service and accords them a non-combat job.
However, the army routinely denies CO status to those who are only opposed to specific wars, such as Webster.
It argues that when a person enters the service he swears an oath and should subsequently fulfil his obligation.
If a person wants CO status, the army says, he can't insist that he is deployed only on his own terms.
This official interpretation has proven contentious.
"There are definitely soldiers out there who specifically object to the war in Iraq, although they would be willing to participate in other wars. They think that it is immoral and wrong"
Centre for Conscience and War
Rights group Amnesty International considers a conscientious objector to be any person who, for reasons of conscience or profound conviction, refuses to perform service in the armed forces or participate in wars or armed conflicts.
These criteria apply to those who are against all wars as well as those who are against specific wars.
McNeil supports this interpretation and says she is lobbying the US Congress to get the army rules changed.
She adds that conscientious objectors come in all shapes and sizes.
Marine reservist Steve Funk, 20, realised he was against all war during his training which included having to bayonet human-shaped dummies while shouting "kill, kill".
Funk said he had a lapse in judgment when he signed up as a 19-year-old, swayed by the recruiters' pitch of new skills, camaraderie and a naive belief that it would be like the Boy Scouts.
The soldier was convicted this year of going absent without official leave, and is currently serving a sixth month jail sentence.
Camilo Mejia, meanwhile, was an experienced soldier who was horrified by what he saw while serving in Iraq.
"The fear of dying has the power to turn soldiers into killing machines," he said in a recent press conference.
Objectors have criticised
America's presence in Iraq
"I went to Iraq and was an instrument of violence. Now I have decided to turn myself into an instrument of peace."
Mejia, who was convicted of desertion, is serving a one year prison sentence.
McNeil says most people who apply for CO status are young and enlist with blinkers on.
"These are folks who are being exploited by some of the best salespeople in the world. They are told that they will get money for a college education and they go in not really thinking about war."
Statistics show this group is comprised of mainly poor whites, black and Hispanics.
The second group, according to McNeil, think they know what war is until they get into a combat situation.
And the third group is made up of people who have combat experience but have become intellectually convinced that war is wrong.
Regardless of the merit of their convictions, conscientious objectors are widely viewed with suspicion within the army.
McNeil says other soldiers can feel threatened by COs because they are essentially questioning the military's raison d'etre.
Others view them as cowardly, unpatriotic or even hypocritical.
At Webster's court martial hearing in May, a colleague, Sergeant-Major John Gioia, testified that some soldiers had reservations about deploying with the sergeant, who converted to Islam in 1994.
"Some of the soldiers, when Webster didn't go, were saying: 'This is great, now we can do our job without having to watch our backs'"
Sergeant-Major John Gioia testifying at Webster's trial
"Some of the soldiers, when Webster didn't go, were saying: 'This is great, now we can do our job without having to watch our backs'," he said.
Webster subsequently complained of victimisation once the reason for his incarceration became known to fellow inmates.
But his wife, Susan, says people shouldn't be too quick to point the finger at those, like her husband, who refuse to fight in Iraq.
She told Aljazeera.net that no one could judge him until "they have walked in his shoes".