<p>Basidiomycota secrete a wide range of enzymes allowing them to break down structural cell-wall carbohydrates present in water-insoluble side streams of the food industry. Fermentation of such side streams by edible fungi represents an alluring option, but methods for quantifying the fungal biomass are required to assess the success of fermentation, as parts of the side streams may still be present at the end of the fermentation. Current methods for quantifying chitin as a marker compound are usually based on photometric assays requiring complex sample preparation and the use of toxic chemicals; therefore, a modified version of the Smith and Gilkerson photometric assay was compared with a semi-automated method that detects the nitrogen compounds remaining after protein hydrolysis using the Kjeldahl method. Mixtures containing fruiting bodies of <i>P. ostreatus</i> and mycelia of <i>L. squarrosulus</i> in defined amounts as well as mycelial samples obtained from bioreactors were analysed by both methods. Comparable chitin contents were obtained above 20–40% fungal content with both methods, and the quantified fungal contents were well reproducible. The semi-automated method has a higher detection limit but is suitable for fungal mycelia and may replace the photometric assay in routine analysis with fungal content above 20–40%.</p>