Data on the influence of substrate composition on the anaerobic degradation of peptone in a bench-scale packed-bed reactor are presented and discussed. The experiments were conducted in a horizontal-flow anaerobic immobilised biomass reactor operated with a hydraulic detention time of 4 h. Peptone was the sole carbon source in the first experiment (E1). In the second experiment (E2), the reactor was fed with peptone and carbohydrates, and in the third experiment (E3), lipids were also added. At end of each experiment, the samples were collected to obtain spatial profiles of the substrates and intermediary metabolites. A modified first-order kinetic expression fits well with the chemical oxygen demand data, allowing kinetic parameter inference in both E1 and E2. The presence of lipids in the E3 influent clearly disturbed the equilibrium of the process, which could be better represented by two first-order kinetic expressions in series. A kinetic model of irreversible first-order reactions (in series and in parallel) with two intermediate products was proposed for representing the entire process. Several modifications of the metabolic routes were clearly represented by the values of the model parameters. It was also possible to conclude that the adsorption of lipids in the fixed bed caused a decrease in the consumption rate of proteins and acetate. Microscopy examinations and fluorescence in situ hybridisation analyses corroborated the conclusions from the kinetic study. The frequencies of the microorganisms changed as the substrate composition was modified, indicating the capability of the microorganisms to adapt.