Chitin and its derived products have great potential in various industries, such as biomedical, pharmaceutical, food, among others, due to its biodegradability, biocompatibility, null toxicity, and versatility. At present, these compounds are obtained by extraction with physical, chemical, or enzymatic processes. The fungus Colletotrichum lindemuthianum DSM 12250 which produces the enzyme chitin deacetylase (ClCDA), is proposed as an alternative for the biotransformation of fungal chitin. Chitin with a % N-Acetylation of 63.6% was obtained from the dry mycelium of Aspergillus niger that, based on analysis of Fourier transform infrared spectroscopy (FT-IR) and Differential Scanning Calorimetry (DSC), is structurally similar to commercial chitin. During fermentation in submerged culture, chitin presence was not found to generate inhibition in microbial growth or the activity of the ClCDA. The maximum enzymatic activity was 0.910 ± 0.002 U/mL and deacetylation of 20.9% were achieved. This was possible due to the enzymatic machinery of the fungus that includes CDA, endo-chitinases, and N-acetyl hexosaminidases. These compounds contribute to decreasing the substrate complexity, obtaining chitosan with a DDA of 57.3%. Submerged culture fermentation of Colletotrichum lindemuthianum DSM 12250 with fungal chitin as substrate represents a potential alternative for integrating different steps in the extraction of chitin-derived products while contributing to a cleaner and more efficient production.