In April 2018 Duffy collected the first Gold medal of the XXI Commonwealth Games in Gold Coast, Australia. Duffy won the women's sprint triathlon by a 43-second lead and became Bermuda's first female Commonwealth gold medalist. She was also scheduled to compete in the women's cross-country mountain bike at the Commonwealth Games, but did not start the event.
Duffy was nominated by the Governor of Bermuda to Queens Birthday List for her services in sport to Bermuda. Duffy received her OBE in November 2018.
Flora Duffy launched The Flora Fund days after winning the inaugural WTS Bermuda in April 2018. Through the fund Duffy hopes to enable youth in Bermuda to pursue their potential, ultimately contributing to a healthier, more ambitious community.