He was due to retire later in 2024 after 12 years as the head of the Construction, Forestry, Maritime and Energy Union (CFMEU) in Victoria.
A union spokesperson said his resignation on Friday evening was due to "relentless stories written with multiple allegations whether true or not about this great union".
Mr Setka said "enough is enough" but did not detail the allegations that prompted his resignation.
"If my stepping down can stop these malicious attacks on our members and officials and allow this great union to continue to fight for our members, for their wages and conditions, so that they go home safely to their families each day, then I'm happy," he said.
John Setka (left) has yet to detail the allegations that have prompted his resignation. (James Ross/AAP PHOTOS)
He said the union remained in the "very capable hands" of the national office and Victorian executive.
Setka garnered a dedicated following and significant influence during his time in the role while also being involved in a string of controversies.
His union leadership came into question in 2019 when then-opposition leader Anthony Albanese moved to expel him from the Labor Party over accusations he said family violence campaigner Rosie Batty's advocacy had led to men having fewer rights.
Mr Setka rejected the allegations and fought his expulsion from the party in court but was cast out months after being convicted of harassing his now estranged wife.
In recent weeks, Mr Setka piled pressure on the AFL to sack its chief umpire and threatened to delay work on the league's construction sites if the sport failed to give in to his demands.
The 59-year-old criticised the AFL for hiring Stephen McBurney, the former head of the now-defunct industrial watchdog the Australian Building and Construction Commission.
In June, Workplace Relations Minister Tony Burke signalled a proposed union demerger bill that would allow the manufacturing division of the CFMEU to split from the broader organisation if supported by a vote.
Mr Setka's time in the top role also coincided with the public breakdown of his marriage to Emma Walters.
Ms Walters was in December 2023 found guilty of threatening to kill Mr Setka in "out of the blue" comments to a private investigator.
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