Embodiments of the present invention are directed to a customizable bio-manufacturing system which includes a manufacturing space having a first air handling system for providing supply air and a second air handling system for handling exhaust air, the supply air system being optionally provided with at least one of filtration, heating, cooling and or humidity control and a plurality of portable modules provided within the manufacturing space. At least one module having an interior capable of being interconnected with another module interior and each module's interior includes one or more components to perform at least one specific task of a biological, chemical, and/or pharmaceutical manufacturing process. At least one module includes an on-board environmental control system for controlling an environment within the module and a connection means for interconnecting the module interior with another module interior. The system also includes a central controller operating to at least perform one or more of operation and information collection for the operation of at least one of the system and one or more modules.