Maize (Zea mays L.) is an important crop in central Thailand where fallow is widely practiced and farmers are interested in crop rotation and beneficial soil biota. A pot experiment using a Typic Paleustult (topsoil + subsoil) from the National Corn and Sorghum Research Centre, Nakhonratchasima Province, Thailand was undertaken over three successive crops to evaluate effects of agronomic practices on populations of arbuscular mycorrhizal (AM) fungi and to determine whether reintroduction of a local Glomus was beneficial to maintain maize yield. The three crops and their treatments were: (1) preceding crop: maize grown in all pots; (2) subexperiment 1: agronomic practices [maize, fallow ± soil disturbance, fallow with solarization, non–AM host (cabbage)]; and (3) subexperiment 2: maize ± Glomus sp. 3 at three rates of P fertilization (0, 33, 92 kg P ha–1). The AM‐fungal community was established under the preceding crop. In subexperiment 1, the three fallow treatments decreased (30%–40%) the total AM spore number in the topsoil whereas there was no change under maize or cabbage. Glomus, the dominant genus, showed sensitivity to fallow. In subexperiment 2, inoculation with Glomus sp. 3 enhanced total AM spore number and root colonization when applied following the three fallow treatments. Furthermore, inoculation promoted grain yield; at nil P following fallow ± soil disturbance, at 33 kg P ha–1 following fallow without soil disturbance, and following solarization. Two treatments, maize following maize and maize following cabbage, did not respond to inoculation with Glomus sp. 3. Overall, the results suggest that reintroduction of Glomus sp. 3, a local AM fungus in this soil, may overcome negative effects of fallow and promote effectiveness of P fertilizer. Further work is needed to evaluate the benefits of other indigenous AM species that persist under modern fertilization practices.