O'Flaherty, who tore a calf muscle last month, clocked 10 minutes and 6.86 seconds in Huelva to finish 11th.
The Rio Olympian, from Newcastle in County Down, is chasing Athletics Northern Ireland's standard of 9:54.00.
Meanwhile, Adam Kirk-Smith clocked 8:47.06 to finish 19th in the men's steeplechase at the same meeting.
Kirk-Smith, who runs for Derry Track Club, is among nine Northern Ireland athletes to have achieved Commonwealth Games consideration standards after posting a personal best of 8:37.62 in Belgium last month.
Athletics Northern Ireland's men's steeplechase consideration standard is 8:43.30.
The majority of those who have achieved Gold Coast standards will have do it again to guarantee their places in the Northern Ireland team.
Kerry O'Flaherty was outside the Commonwealth Games 3,000m steeplechase consideration standard at a meeting in Spain on Wednesday night.