Mission 1 Safe Combination: 451
Location: When you get the hint about the nearby Bone Charm, it’s in a room above you. Back out of the sewer like area and climb up the pipes to enter through a window.
Clue: You find the clue in the bathhouse later. You count the books above the guys desk in his house.

Mission 2 Safe Combination: N/A
Location: This can be found inside Shan Yun’s house, you have to enter for the story. You can learn the secret knock in the florists shop.
Clue: There is a room inside his house with an electrified floor. Disable the traps by using a Whale Oil container that can be found in a nearby room with a breakable door. Once the traps are disabled loot the Release Thy Golden Locks, Gloriana item from one of the glass cases, it’s a musical note that you place in the music devices. Head to the top floor and use it on the Audiograph to open the safe.

Mission 3 Vault Safe Combinations: From left to right as you enter – 011, 235, 813, 455, 891
Location: This is at the very end of the bank mission, inside the vault with 6 different safe’s.
Clue.Christofer Jeorge Safe: – 379
Morgan Yu Safe: 315 (Gem is for a Contract)
Luigi Galvani Safe: 287 (The day Dr Galvani met Anton Sokolov on the 28th Day of the Month of High Cold)
Location: Inside the bank. After you reach the Atrium and disable the electrified fences, take the elevator down to the Lockbox level. There are 3 safe’s in the room with the security chief.
Clue: Dr Galvani’s safe is his birthday. 315 is the amount of coins Morgan Yu had at the bar. 379

Mission 4: There Doesn't Seem to be any safes in this level.

Mission 5 Malchiodi’s Safe Combination: 962
Location: Marked as an optional objective during the final mission
Clue: Symbols on the wall give you the code.