Despite this, Barth reflected that the tutorials provided to explain the game's mechanics had mixed responses, from some players who took up the concept easily to others that remained baffled as to the puzzle's goal even when instructions were set out step by step. They brainstormed a number of puzzles and then eliminated those with similar solutions, and arranged the others into a reasonable learning curve for the game. The team designed puzzles based on general chemistry concepts without envisioning the specific solution that the player would take.

In designing puzzles, Barth wanted to keep puzzles open-ended, allowing the player to come to a solution without funneling them in a specific direction.

The player successfully completes each puzzle by constructing a program capable of repeatedly generating the required output, meeting a certain quota. Similarly, if a waldo delivers the wrong product, the player will need to check their program. While the two waldos can cross over each other without harm, collision of atoms with one another or with the walls of the reactor is not allowed such collisions stop the program and force the player to re-evaluate their solution. The product molecule does not need to match orientation or specific layout of the molecules as long as the molecule is topologically equivalent with respect to atoms, bonds, and bond types however, in larger puzzles, these factors will influence the inputs to downstream reactors. As such, the player is challenged to create a visual program to accept the given inputs, disassemble and reassemble them as necessary, and deliver them to the target output areas to match the required product. The reactors may support specific nodes, set by the player, that act where atomic bonds can be made or broken, where atoms can undergo fission or fusion, or where logic decisions based on atom type can be made.

The two waldos can also be synchronized, forcing one to wait for the other to reach a synchronization command. The commands direct the movement of the waldo, to pick up, rotate, and drop atoms and molecules, and to trigger reactor events such as chemical bond formation. The player adds commands from an array to direct each waldo independently through the grid. Each reactor has up to two input and up to two output quadrants, and supports two waldos, red and blue, manipulated through command icons placed on the grid. The primary game mode of SpaceChem depicts the internal workings of a Reactor, mapped out to a 10 × 8 regular grid.

Spacechem story