The six-times Olympic gold medallist warned his fellow Scots that a split from Great Britain would also mean a split from the lottery-funded training centres that have helped churn out a generation of world-beating cyclists.
"Most of the athletes have had to move to facilities which are often outside Scotland. I had to move down to Manchester because there was not an indoor facility in Scotland," he told the BBC.
"I went to Manchester, trained with the British team and benefited from that. The first thing you have to do if you're really serious about it is you have to provide the facilities and the coaching infrastructure."
Hoy, who retired from cycling last month, did his best to try and avoid getting into the independence debate itself, describing it as a "hornet's nest" and refusing to offer his support to those on either side of the independence debate.
"I don't want to get drawn into it," he explained.
"I've said numerous times how proud I am to be Scottish and how proud I have been to compete for Britain too and I don't think these two things necessarily have to be mutually exclusive."
Hoy also tried to soften the blow of his message slightly, adding that "it would be harder initially to establish themselves" for Scots entering a new training environment, and that, "it's not to say it's impossible but it would just be a different challenge."
But given the huge success of the British Cycling programme - which has housed the best British cyclists together in Manchester for years, and pioneered the famous "marginal gains" programme credited with turning talent into gold - there was no mistaking his mess
"It would not be quite as simple as just saying, 'there is a Scottish athlete, they have won a gold medal, therefore that's a medal for Scotland'," he explained. "In Scotland, we have the Institute of Sport and SportScotland there to try to give support to the athletes. There is support, but it is not quite as simple as saying 'we had x number of medallists from these Games, therefore that will translate into the same medals next time'."