The use of rotations and minimum tillage in agriculture can permit more sustainable production through increasing soil organic matter and nutrients, and breaking of pathogen lifecycles. Soil fungal populations make an important physical and chemical contribution to soil. For example, mycorrhizal species are important in plant nutrition but are often overlooked when considering management practices for efficient soil function. We undertook DNA metabarcoding (Ion Torrent) using novel PCR primers and high-throughput sequencing of the D1 region of the large ribosomal subunit of the rRNA locus, to assess the effect of different forages and cereal tillage methods on the soil fungal community. The study comprised five forage treatments, perennial ryegrass (Lolium perenne) with either low or high N, chicory (Cichorium intybus), red clover (Trifolium pratense) or white clover (Trifolium repens) grown over 3 harvest years (2010–2012). Cultivation of chicory, red clover or white clover led to significantly divergent soil fungal communities, with a notably lower diversity of fungal populations under clover, suggesting a link to soil N dynamics. Consistent with this, was a negative correlation of soil nitrate-N levels with populations of arbuscular mycorrhizal fungi (AMF) and other root-associated fungal groupings (dark septate endophytes, ‘CHEG’, Sebacinales and Ceratobasidiaceae). In contrast, abundance of Fungi belonging to the genera Mortierella and Cryptococcus were positively correlated with soil nitrate-N, with Mortierella also being negatively correlated with soil P. Spring wheat was sown on the same plots (April 2013) followed by winter barley (October 2013). Half of each plot was sown either after ploughing or by direct drilling. A legacy effect of the preceding forage crop on the fungal community was detected after both cereal crops, with plots previously cultivated with ryegrass being most divergent. No overall effect of establishment method on fungal communities was detected but AMF and CHEG fungi were more abundant on direct-drilled plots and pathogenic fungi were more abundant on ploughed plots after the sowing of winter barley.