Skills enable players to gain new abilities, unlock quests and recipes, and increase efficacy and amount of IMG given for performing related tasks. Lower-level skills within the same branch of the skill tree are prerequisites for higher-level skills, and some skills from other branches may be required to learn a skill. An achievement, such as spending an emblem, or an Upgrade Card may also be a prerequisite to learn a skill.

After a player's tenth skill is learned, each additional skill learn takes a compounding 5% increase in the length of time to learn another. So, to learn the twentieth skill will take 63% longer than the base time and the fortieth skill will take 432% longer to learn. The "Increased Brain Power" upgrade cards add to the base number of skills allowed before increases, and each skill category has upgrades available that increase learning speed.

Stoot has said, "The base times have not been changed, but, as discussed in some other forum thread a very long time ago, we finally switched to a system where there are "decreasing returns" — the more skills you learn, the longer it will take to learn further ones."

In the final days of the original Glitch game, skill learning costs were slashed dramatically - skills that had formerly needed days to learn were picked up in hours, so that most players had a chance to complete their skill trees before the game was over.