Horn manure (Preparation 500) is a product used in the practice of biodynamic agriculture. It is obtained by an underground fermentation of cow faecal material incubated in cow horns for several months. The product is used as spray treatment meant to increase soil fertility. In the present report we analyzed the successional changes in bacterial and fungal communities throughout the process of horn manure maturation by high throughput sequencing of ribosomal 16S (bacterial) and ITS (fungal) gene markers. Marked shifts in the microbial community were seen involving a general decrease from a Firmicutes-dominated material to a product transiently enriched in Proteobacteria and later in Actinobacteria, mostly within the Nocardioidaceae family. In the fungal community evolution, the most abundant taxon in the starting faecal material resulted a member of the Onygenales order, known to specifically degrade keratin. Its abundance in the intestine is explained by the fact that keratin, which is also the structural component of hairs and horns, is found in all epithelial layers, including gut mucosae. This occurrence suggests a link of enzymatic/catabolic nature between manure and horn.