Protein-functionalised aluminium nanosheets (PRS–AlNs) were packed in a continuous fixed-bed column to remove crystal violet (CV) and Congo red (CR) dyes. A group of characterisation techniques, like SEM, TEM, AFM, XRD, BET, DSC and Raman spectroscopy, was performed for PRS–AlNs. The influence of several factors like bed depth (1, 2 and 3 cm), inlet dye concentration (50, 100 and 150 mg/L) and inlet flow rate (1.17, 2.26 and 3.34 mL/min) on the characteristics of the breakthrough profile of the adsorption process was examined at optimum pH 9.8 and 3.5 for CV and CR, respectively. The maximum adsorption capacity was achieved as 38.70 and 57.86 mg/g for CV and CR at 1 cm bed depth, 150 mg/L inlet concentration of the dye and 3.34 mL/min inlet rate of flow. The experimental data were analysed using kinetic models like the Yoon–Nelson, Adams–Bohart and Thomas models. Also, a detailed mechanism behind the CV and CR adsorption using PRS–AlNs was proposed in this research work. [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.