Biochar can have a positive effect on agricultural soils and plant yields. The underlying mechanisms that deliver beneficial outcomes are still poorly understood. Soils contain complex communities of hundreds or thousands of distinct microorganisms, and it has been shown that biochar can have an impact on their composition and function. Here we analyse the microbial communities in a controlled field trial that compared the effect of enhanced biochars (EBs) against a farmer practice (FP) of traditional fertilisation (urea, superphosphate and potash) on sweet corn yield. During sequential crop cycles (barley and sweet corn) two types of EBs were applied at low and high levels (total of 1.1 and 5.44 t ha−1, respectively). Samples were taken at the end of a second crop cycle and over 50,000 16S ribosomal RNA (16S rRNA) tag sequences were generated per sample to characterise microbial communities. Despite the lower amounts of nutrients provided by EBs, their amendment to soil produced similar crop yields to the FP. In addition, significant differences in microbial community composition were observed between the high EB and FP treatments. This was driven by differences in the relative abundances of only a few community members. Community level differences were also correlated with a higher soil pH associated with EB laden soil. Network analysis showed that the low EB application had more correlation patterns (co-occurrences and exclusions) between microbial taxa, and highlighted the importance of associations between members of the phyla Acidobacteria and Verrucomicrobia in the biochar environment. Overall, a large number of microorganisms appear to be influenced by EB amendment compared with fertiliser use leading to a complex re-wiring of community composition and associations.