Among the church leaders who have paid tribute to her include the Archbishop of Wales Dr. Rowan Williams, who said she was an "informed Christian".
Dr Williams said the princess had represented the change that has taken place in the Royal Family over the last 50 years.
"The last two years have been humiliating for her, but those who grew up in the 1940s and 1950s would remember a more lively figure."
He said the people across Wales would be remembering Princess Margaret "in particular the little parishes she visited and brought a bit of glamour to."
The recently-installed Catholic Archbishop of Cardiff Peter Smith outlined the princess's considerable contribution to charity work.
She was involved with around 100 charities, many of them for children', he said.
"She was also the first of the Royals to get involved in an HIV charity - something which caused upset at the time".
"Of course, the public image of her was quite different - one of a high-living, high-flying lady who did not always obey the rules."
"Today I and all the churches will be praying for her and for her family."
Flags are still being flown at half mast in tribute to the Princess who had a strong association withWales throughout her life.
Her husband Lord Snowdon's family came from north Wales, and he was the orchestrator of the Prince of Wales's investiture in Caernarfon in 1969.
Later she was to have a love affair with Roddy Llewellyn, the son of Olympic horseman Sir Harry Llewellyn ,who lived near Abergavenny.
Princess Margaret died peacefully in her sleep early on Saturday after suffering another stroke.
Political tributes
A book of condolence at Cardiff's City Hall is open on Sunday until 1700 GMT. It will also be open all week ahead of the Princess' funeral at Windsor on Friday.
Welsh First Minister Rhodri Morgan has spokem of the death as particularly poignant - coming so soon after the 50th anniversary of the Queen's accession to the throne last Thursday.
Welsh Secretary Paul Murphy said she had won the hearts of thousands of Welsh people during her visits.
Princess Margaret was a keen supporter of a number of charities in Wales.
Among them she had been patron of the Cardiff-based cancer charity Tenovus since the early 1960s,.
Tenovus chief executive Marc Phillips said she was a key figure in opening their main research laboratories in Cardiff and Southampton where much of their research work is still carried out.
And Princess Margaret was a patron of the Royal College of Nursing and had great insight into the role and work of nurses, according to the RCN head in Wales, Liz Hewett.
"Nurses in Wales will have fond memories of Princess Margaret because she opened Ty Maeth, RCN headquarters in Wales, in 1965 and visited us again in 1995 to celebrate 30 years of opening," she said.