1. Restoration of high plant species diversity to sites where it has been reduced by intensive grassland management requires identification of appropriate management regimes. Understanding the combinatorial effects of management on above-ground vegetation and below-ground microbial communities will inform management prescriptions on how best to increase plant diversity, restore rare vegetation types and achieve agri-environmental objectives. 2. Changes in vegetation and soil microbial community structure are described from the second phase of a 1990–2004 field trial that investigated the interacting effects of fertilizer and farmyard manure (FYM) treatments imposed after 1998, in the context of previous hay-cut date and seed-addition treatments. 3. Hay-cut date was the main factor influencing plant species composition in phase 1, whereas FYM was the dominant factor in phase 2. 4. Poa trivialis and Lolium perenne increased in abundance with FYM application, particularly in combination with mineral fertilizer, and particularly in 2002 after the 2001 foot and mouth epidemic. The lowest Ellenberg fertility scores were associated with absence of FYM and mineral fertilizer but with addition of seed. 5. The highest plant species diversity in phase 2 was associated with seed addition and the absence of mineral fertilizer, an effect that had probably persisted from phase 1. Progressive development of the target traditional meadow vegetation occurred through phase 2. 6. Fungal:bacterial (F:B) ratios, a measure of changes in the relative abundance of fungi and bacteria in the microbial community, generally increased from 1996 to 2004, and were particularly high in the seed-addition treatments and in the absence of fertilizer. Here the high F:B ratios were associated with species (including legumes) typical of traditionally managed mesotrophic grassland in northern England. 7. Synthesis and applications. These results demonstrate that biodiversity goals for upland meadows need to plan beyond the typical 5–10-year management agreement period of agri-environment schemes. Combination treatments, in which seed addition is vital, alongside appropriate fertilizer, FYM, hay-cut date and grazing regimes, are needed for grassland restoration. However, even after 14 years the most effective treatment combinations had still not restored the target species composition and diversity. The demonstrated change in soil microbial communities, linked to the growth of legumes, might be important to facilitate future increases in plant diversity.