Mr. Nyantakyi himself resigned hours after he was banned by FIFA and a day after government expressed intention to dissolve the association he heads.
His ban comes following an investigative piece from ace investigative journalist Anas Aremeyaw Anas' on corruption in Ghana Football where the GFA boss was caught on camera collecting cash from undercover reporters.
The under coveer journalists also busted 77 Ghanaian referees and 14 Ghana Football Association (GFA) officials allegedly engaging in acts of corruption.
"After a meeting of the Executive Committee this afternoon I chose to resign as President of the Ghana Football Association", Nyantakyi's statement began.
The video also showed Nyantakyi offering to facilitate the award of key government contracts to the businessman on conditions that he paid kickbacks totalling $12 million through him to top officials including President Nana Akufo-Addo.
"I wish to clarify that at no time prior to or subsequent to any deliberations on the video did I consult, contact or inform any government official about discussions on the video".
The Ghana Football Association issued a statement last month backing their president and saying he was innocent until proven guilty.
"The Police Administration is assuring the public of due processes and encouraging persons with verifiable information to volunteer it to Police through the Financial Forensic Unit of the Criminal Investigations Department (CID) headquarters at Accra".
Ghana's Sports Minister Isaac Asiama has stated that the association will be "dissolved with immediate effect", Ghana Web reports.
"As a result of the pervasive nature of the rot within GFA, government, therefore, has chose to investigate the conduct of all officials of the GFA, together with that of the suspended acting Director General of the National Sports Authority (NSA), Robert Sarfo-Mensah, shown in the documentary to be involved in questionable, potentially criminal acts, is, forthwith, referred to the police for further investigation and appropriate action".
"Government will soon announce provisional measures to govern football activity in the country until a new body is duly formed".
Asiamah said the decision had been a hard one to take, and is aware that it is likely to trigger some sort of action from world football's governing body FIFA, who strictly forbid the interference of government in the national federations.
Ghana also risk being suspended from the 2026 World Cup hosting vote next week, when it had been expected to vote for fellow African country Morocco against the joint bid of the United States, Canada and Mexico.
Ghana, who have played at three previous World Cups, missed out on the this year's tournament which starts in Russian Federation on June 14.