Machinarium is a point-and-click adventure set in a mechanical world where the player controls a small robot that has been kicked out of the city. He has to return and confront the Black Cap Brotherhood who terrorizes his kind and took away his girlfriend. The game consists of a number of static, non-scrolling screens the player gets to explore. This is done by clicking on objects in the environment to manipulate them, gathering them in an inventory and solving a wide array of puzzles, ranging from simple item combinations to more complex pattern analysis. The player's robot can scale his height to solve a number of problems, and communication is often presented graphically through speech bubbles that describe a scene using animated images, rather than words.

It is not possible to die, and when stuck, the player can opt to use a single hint (one per screen) or consult a walkthrough book. Pages in this book show the full solution to the level in the form of concept art panels, but to reach it a short side-scrolling shooter mini-game needs to be played. Therefore, the player cannot access it right away. In the beginning progress is done screen by screen, but after a while the world opens up more with many locations available at the same time.