Turkish resort Bodrum was also affected, with McNaughton holidaying in Dalaman further down the coast.
In a post on his official Twitter account, McNaughton wrote: “Jesus just experienced earthquake in Turkey, literally c****** myself room shaking all over place, just stood outside now no sure what to do.”
He described being afraid the building would fall down – adding that he “grabbed the kids and done [sic] a runner wasn’t fun at all”.
McNaughton is best known for his time at the Bluebirds, where he earned icon status in a nine-year stint.
He retired last season following a one-year spell at Inverness Caledonian Thistle in his homeland.
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The Scot insisted he was looking forward to a new challenge after his Cardiff testimonial in March.
McNaughton, 34, said: "Have decided to call time on my playing career, have loved every minute of it.
"Looking forward to spending a bit of time with the family and then start look for a new challenge to sink my teeth into.
"Big thank you to everyone that's helped me along the way, family, friends, teammates, coaches and fans.
New aftermath video shows damage and rising floodwater on Kos after Turkey earthquake
"Feel privileged to have played at some great clubs along the way and to have played for 17 years I feel very fortunate.
"Felt right to play my last game for Aberdeen, the team where it all started for me on Saturday.
"Good luck to all my mates still playing I hope you have a great season and look forward to come watching you at some point this season."
Moment toddler is almost trampled as people flee cafe during Turkey earthquake
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