The present study focuses on process imbalances in Danish centralized biogas plants treating manure in combination with industrial waste. Collection of process data from various full-scale plants along with a number of interviews showed that imbalances occur frequently. High concentrations of ammonia or long chain fatty acids is in most cases expected to be the cause of microbial inhibitions/imbalances while foaming in the prestorage tanks and digesters is the most important practical process problem at the plants. A correlation between increased residual biogas production (suboptimal process conditions) and high fractions of industrial waste in the feedstock was also observed. The process imbalances and suboptimal conditions are mainly allowed to occur due to 1) inadequate knowledge about the waste composition, 2) inadequate knowledge about the waste degradation characteristics, 3) inadequate process surveillance, especially with regard to volatile fatty acids, and 4) insufficient pre-storage capacity causing inexpedient mixing and hindering exact dosing of the different waste products.