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Filamentous fungi are employed for the large-scale production of value-added products, including organic acids, enzymes, and antibiotics and bioprocess characterization is essential for production optimization but relies on empiricism-based strategies. Protein expression profiles in an industrial scale, 180 h fed-batch fermentation of Penicillium chrysogenum are presented. The biomass of P. chrysogenum, as well as the specific penicillin V production rate and fungal morphology were monitored during fermentation to be compared with obtained protein profiles. Our results demonstrate a correlation between proteomics data and biomass concentration, morphological changes, and penicillin production.