The former Catholic leader and five others were arrested under a sweeping national security law that Beijing imposed in 2020 after the outbreak of protests in the semi-autonomous Chinese city.
An high-profile Catholic Cardinal from Hong Kong was among six dissidents who have been convicted over their running of a multi-million-dollar defence fund for arrested anti-government protesters.
On Friday, five of the group were fined an equivalent of $500 each for the crime of failing to properly register the fund as a society, while a sixth got a smaller fine.
Cardinal Joseph Zen, one of Asia's highest-ranking Catholics, is among the scores of veteran activists facing legal threats as China stamps out protest in the former British colony.
The six were arrested under sweeping national security legislation that Beijing imposed in 2020, a year after the outbreak of huge and often violent protests.
They are yet to face charges under that law, which can carry a sentence of up to life in jail.
Among Zen's co-convicts on Friday were activist and singer Denise Ho, and veteran human rights barrister Margaret Ng. All had pleaded not guilty, setting up a two-month trial.
On Friday, magistrate Ada Yim found "the only and irresistible inference" was that the fund was a "local society" and so subject to the rules.
Speaking outside the court, Ng said it was the first time anyone had been convicted for failing to register a society, adding that it was "extremely important in relation to the freedom of association in Hong Kong".
"The effect to other people, to the many, many citizens who are associated together to do one thing or another, and what will happen to them, is very important."
Cardinal Zen's arrest earlier this year, for "colluding with foreign forces", shocked the city's Catholic community and renewed criticism of the Vatican's warming ties with Beijing, including from fellow senior clerics.
Zen, who is now retired, had clashed with Pope Francis' policy towards China, as he opposes warmer ties with Beijing.
The pope has defended Vatican's relationship with China saying that he has "chosen the path of dialogue, open to dialogue" with the world's most populous country.
Outside the court on Friday, Zen noted the concern overseas but insisted he was acting in his role as a humanitarian, not a cardinal, adding that "Hong Kong has not seen any damage to its religious freedom".
Zen's group acted as trustees and secretary of the now-defunct "612 Humanitarian Relief Fund", which helped pay legal and medical costs for people arrested during the 2019 unrest.
The fund disbanded last October after national security police demanded it hand over operational details, including information about its donors and beneficiaries.
Prosecutors revealed in court that the fund had raised as much as $34.5 million (HK$270 million) from more than 100,000 separate donations.
They said "part of the fund was used for political activities and non-charity events", including donations to protest groups and activists overseas.
The defence argued that the fund was "merely a name given to a sum of money" and the defendants did not form any society.
It also challenged the law's vagueness, saying it imposed disproportionate restrictions on the freedom of association.
"The criminalisation for failure to register is undoubtedly a curb on these important freedoms for civil society," defence counsel Gladys Li said.