The Podmoskovie was commissioned in 1986 and has been modified over the last 20 years to conduct special missions.
Podmoskovie was pictured leaving its port in Severodvinsk Russia on October 22, the National Interest reports.
The submarine and her sister BS-136 Orenburg are Russia’s answer to the US Navy’s secretive Seawolf-class submarine USS Jimmy Carter.
Carter is able to launch and recover various unmanned vehicles and can support special operations forces.
Putin’s Podmoskovie is thought to be similar but few details about the spying submarines are known.
In July experts warned that Russia has subs patrolling the world that reportedly breached UK waters by approaching the Royal Navy’s base in Faslane, Scotland.
Andrew Metrick, who co-wrote the report for the Center for Strategic and International studies, said: “Russia operates a small number of very small, nuclear powered submarines that are capable of diving in excess of several thousand meters.
“You can imagine what a clandestine deployable deep submergence vehicle could be used for.
“It’s pretty scary to think about some of the types of missions.”
After Podmoskovie entered the port in 1999 it had is missile tubes removed three years later.
The submarine also appears to have had her hull lengthened.
It is thought Podmoskovie can launch and recover unmanned underwater vehicles which dock on top where the missiles used to be located.
One of the unmanned subs is called a Klavesin-1R and can dive to depths of nearly 20,000ft.
It is also thought to host a secretive AS-12 Losharik – a nuclear-powered mini-submarine designed for intelligence and special operations.
Very little is known about Losharik but it is thought it is tasked with tapping undersea cables.
Podmoskovie’s return to open water comes as Russia unveiled it’s “Satan 2” nuclear missile to world.
The atomic warhead can carry payloads 1,000 times more powerful than those dropped on Japan at the end of WWII.