Brailsford's inspirational leadership is credited with turning Great Britain into a dominant force in track and road cycling in the space of just eight years.
Great Britain won seven gold medals, one silver and one bronze from the ten track cycling events at London 2012, while they also won gold, silver and bronze across the four road events.
Brailsford has already hinted that he can't combine his position as British Cycling's performance director with his principal role at Team Sky and that he was preparing to readjust his responsibilities after the Olympics.
But Moynihan is confident Brailsford, who also guided Bradley Wiggins to a first British Tour de France win last month, would plan for the moment of his succession with trademark meticulous attention to detail.
"He is a leader of a team and all the people in that team have benefited from his expertise. Within that team will be people who have come through a system which is totally focused on performance and delivery," he said.
"I'm glad to say that the work that he's done has improved cycling, if he decides to move on will we miss him? Of course.
"The legacy he would leave for cycling would benefit the sport for many years to come."
Meanwhile, Moynihan has continued his call for the BOA to be at the centre of UK Sport’s administration following a successful Games for home athletes.
He has already called for a shake-up of school sport and government sports policy and now wants the way British sport is run to be simplified.
"It is a highly complex over-bureaucratic, overlapping set of different bodies and acronyms and it needs massive simplification," he said.
"The principle is to then empower the ones that are doing so well, empowering the clubs, empowering the governing bodies and where they need help, they are given help."