Integrating intercropping with green manure within crop rotation offers a sustainable pathway to enhance soil microbial diversity and overall agroecosystem health. This study evaluated the effects of diverse fertilisation practices on the soil microbiome in a barley (Hordeum vulgare L.) cropping system following the incorporation of an oat-vetch (Avena sativa and Vicia sativa) and green manure incorporation versus single cropping of oats. The field experiment took place at the Agricultural University of Plovdiv, Bulgaria. Using high-throughput metagenomic sequencing, we assessed the structure and functions of the soil microbial community. The fertilisation treatments included mineral fertiliser, vermicompost, a combination of vermicompost and mineral fertiliser, and biochar, along with a non-fertilised control. The investigation compared two preceding cropping systems before barley cultivation: an oat-vetch intercrop used as green manure, incorporated into the soil at the ripening stage, and a conventional approach where barley was sown directly without prior green manuring. All treatments were conducted in triplicate. Sequencing allows for detailed taxonomic and functional profiling. The most abundant bacterial phyla identified were Actinobacteriota, Proteobacteria, and Bacteroidota, with Actinobacteriota showing increased abundance under fertilised conditions. Soils treated with compost and compost-mineral mixtures exhibited notably higher alpha diversity. Beta diversity analyses (PCA, PCoA, UPGMA) revealed clear differences in microbial community structure among the treatments. Certain genera, such as Sphingomonas, Noviherspirillum, and Agromyces, were particularly enriched in soils receiving vermicompost or green manure. Their presence suggests enhanced microbial functionality and nutrient cycling in those plots. Overall, the combination of green manure and organic inputs supported more diverse and functionally active microbial communities, contributing to the resilience and sustainability of barley-based cropping systems. This study focuses on the bacterial component of the soil microbiome; nutrient cycling and soil health are governed by the combined interactions among bacteria, fungi, and protozoa.