Turkey's post-coup purge targets 120 company heads
The raids are the latest in the ongoing purge that has followed the failed July 15 coup.
The companies targeted are accused of channelling money to the self-exiled cleric, who Turkey's government says was behind the putsch attempt.
Gulen has denied the charges and has called for an international inquiry into the failed coup.
These latest raids come after President Recep Tayyip Erdogan pledged earlier this month to uproot the "nests of terrorism" that support Gulen - a phrase he used to refer to schools, businesses and charities linked to the cleric.
It was in the sphere of business, however, that Erdogan claimed Gulenist activity was strongest.
"We will cut off all business links, all revenues of Gulen-linked business. We are not going to show anyone any mercy," he said.
Companies raided on Tuesday included contracting firm Akfa Holding and the A101 supermarket chain in the Uskudar and Umraniya districts, Anadolu reported.
Akfa Holding's chairman, Fatih Aktas, was among the dozens of company heads arrested on Tuesday.
Aktas was detained along with other employees of the firm who are accused of helping transfer 'himmet money' - money collected as charitable donations - to Gulen between 2011 and 2015.
Since July 15, around 26,000 people have been arrested across Turkey as President Erdogan has tightened his grip over the country.
Arrests have reached military leaders, members of the judiciary, teachers and public servants.
A further 82,000 people have been dismissed or suspended from their jobs for alleged links to coup plotters.