The use of biochar in agricultural soils has received increasing attention over the last decade and enhancing biochar through chemical modification offers a strategy to reduce the amount of biochar required for improving soil productivity. However there is limited knowledge on how mineral enhanced biochars alone, or in combination with conventional fertilisers impact on microbial processes and edaphic parameters of soil or the root, and how this influences agricultural yield in the long-term. To investigate this we assessed crop yield, edaphic parameters and microbial communities within the bulk soil and on roots at the end of the third crop-cycle from a long-term agricultural trial where pre-existing enhanced biochar applications (from previous crop-cycles) totalled between 0 and 5.5 t ha−1 and were then supplemented with fresh enhanced biochar (0.1 t ha−1) and traditional N fertiliser (50 kg ha−1) in a crossed design. We found an array of effects associated with existing and new enhanced biochar applications in conjunction with N fertiliser on plant yield, soil nutrients and microbial communities. Yield decreased up to 27% with any soil amendment and was greatest in the unamended control. Soil nitrate increased from 30.4 to 59.6 mg kg−1 due to N fertiliser with little effect of the enhanced biochar. Soil pH increased from 4.59 to 4.86 due to previously applied enhanced biochar and was associated with applications of at least 1 t ha−1. There were differing responses in the microbial communities between bulk soil (294 taxa changes) and roots (383 taxa changes) to the fertilisation regimes, which were unrelated to the nitrate content in the soil and appeared to be driven by pH changes, especially for communities associated with plant roots. This has important implications on which soil compartments should be investigated in future studies of microbial communities. The short- and long-term effects of enhanced biochar observed here question the relevance of studies examining once-off applications of biochar and their extrapolation to real world scenarios i.e. where sequential application of biochar might occur. It is likely that responses of agricultural systems may depend on the historical use of biochar.