Native of nearby Parappanangadi, Hamsakoya (61) had settled in Mumbai. He and his family had come down to his hometown on May 21 and had been under quarantine.
Hamsakoya's five family members have also tested positive and are undergoing treatment.
Malappuram District Medical Officer Dr K Sakeena said Hamsakoya's wife and son showed symptoms of COVID-19 first and were admitted to the hospital.
All possible medical care was given to the deceased, but he breathed his last early this morning, she said.
"His wife and son tested positive for the virus first in his family. Later, Hamsakoya was also tested positive for the virus and had been under treatment at the medical college.
His daughter-in-law and two of his grandchildren have also tested positive and are under medical observation," Dr Sakeena said.
A veteran footballer of the Malabar region, Hamsakoya had played for Maharashtra state in Santosh Trophy in the 1980s.
A wing back during his playing days, he was called up for the national team camp twice but never played for the country.
"We mourn the loss of former footballer Hamza Koya, who lost his battle against COVID-19 in a Malappuram hospital today. He had represented Maharashtra in the Santosh Trophy, and had been called up for the National Team camps on 2 occasions," the All India Football Federation said in a tweet.
Hamsakoya started his football his career with Western Railway and went on to play for other Mumbai clubs like Union Bank, RCF, Tata Sports and Orkay Mills.
"His last club was Orkay Mills. He was a very hard tackling defender, also good at aerial balls," former Mumbai footballer Prakash Shetty, who played with Hamsakoya at Union Bank and Orkay Mills, said.
Hamsakoya never played in Kerala in any official tournaments under the aegis of the state football association.
The mortal remains of the deceased would be buried as per the COVID-19 protocol, sources said.
Photograph: Indian Football Team/Twitter
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