Anaerobic wastewater treatment is, in many cases, a justified alternative to typical activated sludge processes, from a technological, economic, and ecological point of view. The optimisation of fermentation reactors is primarily concerned with increasing the biodegradation of organic compounds and biogas production, as well as improving efficiency in the removal of nitrogen and phosphorus compounds. The aim of the research was to determine the impact of using low-cost recycled filling on the efficiency of treating real confectionery wastewater in a vertical anaerobic labyrinth flow bioreactor. The experiments focused on selecting the organic loading rate that would allow for the effective biodegradation and removal of pollutants, as well as the efficient production of biomethane. It was found that the tested reactor can operate efficiently at a maximum organic loading rate (OLR) of 7.0–8.0 g of chemical oxygen demand (COD)/L·d. In this OLR range, high efficiency was guaranteed for both wastewater treatment and biogas production. However, increasing the OLR value to 8.0 g COD/L·d had a significant negative effect on the methane (CH4) content in the biogas. The most efficient variants achieved a biodegradation efficiency of around 90% of the organic compounds, a CH4 content of over 70% in the biogas, and a biogas yield of over 400 L/kg of COD removed. A significant influence of the applied OLR on the ratio of free organic acids (FOS) to total alkaline capacity (TAC) and pH was observed, as well as a strong correlation of these indicators with the specific biogas yield and CH4 content. The application of a solution based on the use of a hybrid system of anaerobic granulated sludge and an anaerobic filter resulted in an efficient treatment process and an almost complete elimination of suspensions from the wastewater.