Batch processes are inherently irreversible. In fact, design parameters and initial states can affect irreversibility and controllability of a batch process. Current design methodologies do not include controllability as a criterion for process specification. In this work, the case of Bacillus thuringiensis process is studied in batch operation, and its operational conditions are defined according to a phenomenological-based model. Regarding process design, a novel methodology is presented using set-theoretic methods and a controllability index to find the best design parameter and initial state values. Using this methodology the controllability index is doubled improving the dynamic behavior of the process.