The Nightshift Code is a hidden object game with puzzles between each chapter.
As usual, the player has to find objects of a list in a series of cluttered screens. At the start of each screen, a bonus points counter at the bottom-left starts to decrement slowly, acting as a timer. Clicking on wrong spots also subtracts points. If it reaches zero the chapter is restarted, and the player must find all the objects and solve any puzzle again.
Each level has a scavenger hunt where a list is shared by several screens. A navigator at the bottom-right allows the player to jump between locations.
The game has two modes: story and arcade. Story mode has a plotline that is revealed through comic book panels before and after each screen and puzzle. In arcade mode a timer replaces the bonus points. The objective is to complete each screen as quickly as possible.
There are two puzzles: the logoscope and a cryptogram. The logoscope contraption compares two sets of clues to decode symbols. The player deducts their meaning and places the symbols in labeled slots around the screen. The game rejects the wrong ones. The cryptogram shows a coded message using objects instead of letters. The message is decrypted by placing the correct objects in letter bins around the screen.