Nickel is one of the most dangerous environmental pollutants and its removal from wastewater is an important task. The capacity of a mineral–organic hybrid adsorbent, consisting of Shewanella xiamenensis biofilm and zeolite (clinoptilolite of the Chola deposit), to remove metal ions from nickel-containing batch systems under different experimental conditions was tested. The obtained biosorbent was characterized using neutron activation, SEM, and FTIR techniques. It was established that maximum removal of cations, up to 100%, was achieved at pH 6.0. Several mathematical models were applied to describe the equilibrium and kinetics data. The maximum adsorption capacity of the hybrid biosorbent, calculated using the Langmuir model, varied from 3.6 to 3.9 mg/g. Negative Gibbs energy values and positive ∆H° values indicate the spontaneous and endothermic character of the biosorption process. The effects of several parameters (pH and biosorbent dosage) on Ni(II) removal from real effluent, containing nickel with a concentration of 125 mg/L, were investigated. The optimal pH for Ni(II) removal was 5.0–6.0 and an increase of sorbent dosage from 0.5 to 2.0 led to an increase in Ni(II) removal from 17% to 27%. At two times effluent dilution, maximum Ni(II) removal of 26% was attained at pH 6.0 and sorbent dosage of 1.0 g. A 12-fold effluent dilution resulted in the removal of 72% of Ni(II) at the same pH and sorbent dosage values. The obtained hybrid biosorbent can be used for Ni(II) removal from industrial effluents with low Ni(II) concentrations.