CLUE: Accusations and Alibis is a hidden object game that is an adaptation of a classic board game. The aim of the game, just like in the original, is to discover who the murderer is, what weapon was used and in what room the crime took place before time runs out. Each room in the mansion is a separate hidden object area where the player must find all the items from the list at the bottom of the screen.

After clearing one of the rooms, a screen appears that starts a rumor about one of the suspects, weapons and rooms. Suspects give clues about the case based on this rumor.
There are four tabs at the top of the screen: Game Map, Checklist, Evidence, and Clue Log.
The game map shows an overhead view of the mansion with all the rooms visible, where the player can choose where they want to go after completing one of them.
In the checklist, the player can mark suspects, weapons and rooms to track the progress of the case. When a suspect reveals important information, the game automatically crosses out that item.
In the evidence tab, the player can view items found in each room.
The last tab is the hint log, which contains all the hints received so far.

Finally, after examining all the rooms, the game will display the accusation screen, where the player must indicate who the murderer was, what weapon was used and in which room the crime took place.