Chitosan is a major structural component of fungal cell walls and has diverse medical and other applications. However, cost‐effective culture and extraction methods for fungi need to be developed. Therefore, Mucor rouxii was grown on YPG‐media in both submerged batch and semi‐continuous cultures. Chitosan was extracted from the mycelia to explore strategies to enhance yields and production rates. As observed in earlier studies, M. rouxii is able to adapt to shear stress when cultured semi‐continuously. Modeling the hyphal growth of batch experiments shows that the mycelia were ruptured by shear forces within a short cultivation time shown by a decreased hyphal length. However, an increasing chitosan content was observed with an increasing cultivation period in semi‐continuous cultures, which is an indication for the adaption to shear stress. Semi‐continuous culture resulted in the highest contents of extractable chitosan. The results and models of hyphal growth, including tip extension and branching, suggest that repeated batch cultures may be optimal for chitosan production.