The fate and effect of the herbicides linuron and metribuzin on the co-composting of sewage sludge and green waste were addressed in this work. The experiments were conducted in metal cubic containers of 1.0 m3 volume simulating a windrow composting system. A mixture of sludge and green waste was prepared at a ratio of 1:5 v/v. The mixture was split in four equal parts and the two herbicides were added, using a pressure sprayer, as sole or mixed pollutant in each of the three mixtures. The forth mixture was composted without any addition of herbicide, to serve as control. Temperature, physicochemical characteristics, herbicide concentration, carbon dioxide emission, methane emission and microbiological parameters were measured either daily or every time the mixtures were turned, for a period of 80 days. Both herbicides’ concentration decreased significantly resulting in removal efficiencies of 99.1–99.7% and 95.8–96.0% for linuron and metribuzin, respectively. Incubation of microbiologically inactive mixtures at a temperature schedule following the spontaneous temperature evolution in the composters resulted in very little (1–11%) decomposition for both herbicides. Comparison of the variation of physicochemical parameters and microbial populations during composting indicated that both herbicides did not affect the composting process.