Thirty-year-old Sami Karnaz of Mississauga was arrested with the help of Peel Police, Hamilton police said in a statement early Sunday.
Karnaz has been charged with arson and disregard for human life.
The fire broke out at a former 7-Eleven at the corner of Ashford Boulevard and Main Street East, which was being turned into a Subway restaurant.
"Shortly before 4 a.m., we got a call there was a fire and a possible explosion," said Staff Sgt. Jack Longhorn. "When we got there the place was totally involved with flames."
Police say one employee working on the renovation of the building cannot be accounted for at this time.
The building was gutted and heavily damaged by the fire, so its entire structure is collapsing.
As the building is so unstable, work crews have yet to start sifting through the rubble. Heavy equipment is being brought in to help with the investigation Sunday morning, police say.
The homicide unit continues to investigate. Anyone with information is asked to call Det. Randy Kovacsik at 905-546-3836 or Crime Stoppers.