The aim of this work was to evaluate the impact of different N-rich animal wastes on the composting of ligno-cellulosic wastes by a range of classical and novel methods, with particular emphasis on microbial community composition. Two composting mixtures were prepared by adding to a mixture of cotton carding wastes and wheat straw: (i) meat and bone meal and (ii) blood meal and horn and hoof meal. Composts were analyzed using physico-chemical and biochemical properties, as well as nucleic acid microarrays. Results showed that physico-chemical and biochemical parameters differentiated composts depending on their degree of stability, while microarray hybridization discriminated compost samples according to the starting materials used in the compost production. Microarray analysis indicated not only the presence in the composts of bacteria involved in N(2) fixation and plant disease suppression, but also the presence of Acinetobacter calcoaceticus that is suspected to trigger an autoimmune response related to bovine spongiform encephalopathy. The present work highlights the importance of using parameters addressing different properties of the composting matrix for a proper evaluation of the process performance.