The last 10 years have seen serious rifts in the Anglican Communion over homosexuality and the consecration of women bishops.
The US in particular saw the departure of Anglican parishes from the US Episcopal Church after the consecration of its first openly gay bishop in 2003.
In the Church of England, moves to consecrate women bishops led three bishop and several parishes to join an Ordinariate set up by the Roman Catholic Church.
In 2010, the Archbishop floated the idea of a Covenant designed to prevent the break-up of the Communion, but the proposed bandage to the Communion's wounds ended up being nearly as divisive as the rifts it was intended to heal.
In an interview with the Press Association following his resignation, Dr Williams said: "The worst aspects of the job I think have been the sense that there are some conflicts that won't go away, however long you struggle with them.
"And that not everybody in the Anglican Communion or even in the Church of England is eager to avoid schism or separation.
"I've certainly regarded it as a real priority to try and keep people in relationship with each other. That is what bishops have to do - what archbishops above all have to do."
The Archbishop admitted that the row over gays had at times been a "nuisance" as he endeavoured to maintain relationships across the Communion.
"Crisis management is never a favourite activity, I have to admit, but it's not as if that has overshadowed everything," he said, when asked if he was relieved to be going.
"It's certainly been a major nuisance, but in every job that you're in, there are controversies and conflicts and this one isn't going to go away in a hurry. So I can't say that there's a great sense of 'free at last'."
At times, Dr Williams himself was the source of division in the Church. In 2008, he sparked controversy when he suggested that aspects of Sharia law, such as those relating to marital disputes or financial matters, should be incorporated into the British legal system.
The Archbishop admits now that his argument "could have been clearer", but maintains that it was a question "which needed discussion".
"I reread quite recently the text of the lecture on Sharia law, and I still stand by the argument of it," he said.
"I was a bit taken aback by the violence of the reaction [but] I feel that an important point was raised, a point about how the single law of the land works with and legitimates other kinds of jurisdiction of jurisdiction within it, which already happens.
"The word 'sharia' is, of course, very emotive for people and in spite of attempts to explain that it doesn't mean what a judge in Saudi Arabia might think it means, people still have that image in their minds. That's where I could have been clearer, I'm sure."
His time as spiritual leader of the Anglican Communion also saw the emergence of an increasingly vocal and bold atheist movement which began to challenge not only the existence of God, but the very presence of Christianity in public life, from the spheres of education to the House of Lords.
Last month, the Archbishop and prominent atheist Richard Dawkins drew hundreds of people young and old to an amicable debate at Oxford University on the origins of the universe.
Reflecting on his willingness to debate with atheists, Dr Williams said there was a "great deal of interest still" in the Christian faith.
"I don't think Christianity is losing a 'battle against secularisation'," he said.
"I certainly don't get that impression when I'm with congregations, when I'm in church schools or in many other settings like that - even when I'm in a very mixed group, let's say, of 6th formers."
Possibly referring to the recent court cases involving Christians who faced disciplinary action for wearing the cross at work, the Archbishop said there was still "a lot of ignorance" and "rather dim-witted prejudice" surrounding the visible manifestation of Christianity "which sometimes clouds the discussion".
"I don't think that there's somehow a single great argument that the Church is losing," he said.
"I think people have come back to debate, quite properly, with Richard Dawkins, with Philip Pullman, with Tony Grayling and others - that argument goes on very robustly.
"What I think slightly shadows the whole thing is this sense that there are an awful lot of people now of a certain generation who don't really know how religion works, let alone Christianity in particular.
"And that leads to confusions and sensitivities in the wrong areas – you know, does wearing a cross offend people who have no faith or non-Christians? I don't think it does, but people worry that it will, and that's partly because there's a slight tone-deafness about how religious belief works.
"So, yes there's a challenge, and yes the Church's public role is more contested than it used to be, and yes we have to earn our right to speak more than perhaps was once the case. But that's probably good for us."
Reflecting on the more positive aspects of his time as Archbishop of Canterbury, Dr Williams said it had been a "privilege" to see grassroots churches around the world.
"The privilege is that you're taken into the heart of the local church's life for a few days. You see what really matters to people in parishes and schools and prisons and hospices and so forth. I think there must be very few jobs where you have quite that degree of 'open doors' for you."
The two things he could look back on with the greatest satisfaction, he said, were the launch of Fresh Expressions and the Anglican Alliance of relief and development agencies.
Dr Williams will stay in his role until the end of December. In January next year, he will take up a new position as Master of Magdalene College, Cambridge.
He did not come down on who he would like to see fill his shoes, except to say that he would like the next Archbishop of Canterbury to be the one "God would like".
"I think it's a job of immense demands and I would hope that my successor has the constitution of an ox and the skin of a rhinoceros really!" he quipped.
"He will, I think, have to look with positive, hopeful eyes on a Church which, for all its problems, is still for so many people a place to which they resort in times of need and crisis, a place to which they look for inspiration and I think the Church of England is a great treasure.
"I wish my successor well in the stewardship of it."