Modular, free-standing cleanrooms have many distinct advantages over the fixed wall counterparts. Using modular rooms greatly reduces design, engineering, and construction time, thereby reducing costs. Since they are not an integral part of a larger structure, modular rooms can be taken down and moved to other facilities, or even sold as an asset. Fixed wall cleanrooms do not have this flexibility.

Expanding a modular cleanroom can be easily accomplished by taking off a wall and adding another module. The prefabricated design allows the room to be expanded, relocated, or reconfigured into a different shape or made into multiple smaller rooms.

All air handling and filtration equipment modules are built into the modular room ceiling. Hook-ups for electrical and plumbing are engineered in as part of the design.

The amount of time it takes to construct a modular room is much less than constructing a permanent walled structure. It can take several months to construct a fixed wall cleanroom because of the amount of design, engineering, and the various trades involved. However, a fairly sophisticated modular room can be constructed in a week or even less that with experienced workers. Onsite assembly of a modular cleanroom is also less disruptive to surrounding operations in comparison to their fixed wall counterparts.

Meanwhile, modular cleanroom can be upgraded easily by adding fan filter units to the top of the equipment, instead of verifying the whole design compare to cleanroom project.