GCMB is currently looking for a replacement and, once selected, Doheny will work closely with them to enable a smooth transition into the role.
Doheny will be on secondment to the Glasgow Organising Committee until September, where she will assist in accommodating official client groups attending the games.
She will also assist in identifying a Games travel provider and select hotels to accommodate VIPs visiting the Glasgow 2014 Commonwealth Games.
GCMB chief executive Scott Taylor said: "Molly has made a fantastic contribution to Glasgow and has played a major part in the city becoming Scotland’s conference capital.
"She has built up an exceptional team whose professionalism and expertise are recognised by conference clients and meetings industry professionals alike.
"While we are obviously sad to see Molly leave GCMB, we fully understand her reasons for doing so and wish her the very best in her future plans."
Doheny said that retiring from kthe GCMB had been a "difficult decision" to make.
"However I do so in the knowledge that I leave behind a highly motivated, focused and world class conference sales team who will ensure that Glasgow’s reputation as a global meetings centre continues to go from strength to strength and I am delighted to have the opportunity to work with Glasgow 2014 in the coming months." she added.