The goal of Machinarium is to solve a series of puzzles and brain teasers. The puzzles are linked together by an overworld consisting of a traditional "point and click" adventure story. The overworld's most radical departure is that only objects within the player character's reach can be clicked on.
Machinarium is notable in that it contains no dialogue, neither spoken nor written. The game instead uses a system of animated thought bubbles. Easter egg back story scenes in the same format can only be revealed by idling in certain areas.
The game employs a two-tier hint system. Once per level, the player can receive a hint, which becomes increasingly vague as the game progresses. Machinarium also comes with a walkthrough, that can be accessed at any time by playing a minigame. As with dialogue, the walkthrough is not in written or spoken form, but instead a series of sketches describing the puzzle at hand and its solution. However, the walkthrough only reveals what must be done in that area, and not how that puzzle relates to the game chronology.