Authorities said the 31-year-old - nicknamed "Speedy" Gonzalez - suffered "gunshot wounds" in an attack inside a house in the coastal province of Esmeraldas, which borders Colombia and is plagued by rival drug gangs.
Police did not specify a motive for the crime.
A second victim, who was not identified, died while being rushed to hospital.
Ecuador is nestled between the world's biggest cocaine producers, Colombia and Peru, and has become the departure point for 70 percent of the world's supply of the drug.
With an influx of gangs, the homicide rate rose from six per 100,000 people in 2018 to a record high of 47 in 2023, before dipping to 38 last year.
Two players from the second-division team Exapromo Costa FC, Maicol Valencia and Leandro Yepez, were shot in an armed assault in the southwestern coastal city of Manta on September 10.
Valencia died in the gunfire, while Yepez succumbed to his injuries two days later.
The club said the players were victims of an attack directed at another target.
A player for the second-division team 22 de Julio FC, Jonathan Gonzalez previously played to Olimpia in Paraguay and Leon in Mexico.
The Ecuadorian Football Federation (FEF) and local clubs expressed condolences to the footballer's family.