Addition of food waste (FW) as a co-substrate in anaerobic digesters of wastewater treatment plants is a desirable strategy towards achievement of the potential of wastewater treatment plants to become energy-neutral, diverting at the same time organic waste from landfills. Because substrate type is a driver of variations in phylogenetic structure of digester microbiomes, it is critical to understand how microbial communities respond to changes in substrate composition and concentration. In this work, high throughput sequencing was used to monitor the dynamics of microbiome changes in four parallel lab-scale anaerobic digesters treating sewage sludge during acclimation to increasing amount of food waste. A co-occurrence network was constructed using data from 49 metagenomes sampled over the 161 days of digesters' operation. More than half of the nodes in the network were clustered in two major modules, i.e. groups of highly interconnected taxa that had much fewer connections with taxa outside the group. The dynamics of co-occurrence networks evidenced shifts that occurred within microbial communities due to the addition of food waste in the co-digestion process. A diverse and reproducible group of hydrolytic and fermentative bacteria, syntrophic bacteria and methanogenic archaea appeared to grow in a concerted fashion to allow stable performance of anaerobic co-digestion at high FW.