The three, comprising one Turkish national and two men from Russia's volatile Caucasus region of Dagestan, were detained in raids on Friday and remanded in custody by a court yesterday, the Dogan news agency said.
Items including suicide belts packed with explosives, camouflage gear and military knives were seized by the authorities, it added.
The three had been planning to attack a rally around Istanbul's Taksim Square promoting transgender rights.
The gathering took place on Sunday but was broken up by police, Dogan said.
The Istanbul authorities had broken up the transgender rally after banning that event as well as a larger gay pride rally planned for the coming Sunday.
It had cited security reasons and safeguarding public order as the reason for the ban.
Istanbul has twice been hit this year by deadly attacks blamed on IS.
A blast in Istanbul's historic centre in January killed a dozen German tourists while an attack on the Istiklal Street shopping hub in March killed three Israelis and and Iranian.
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