The use of acid soil-tolerant annual legume pasture species and liming to raise soil pH can have legacy effects that improve subsequent wheat crop growth in acid soils. We established a two-year experiment in a semi-arid environment with and without historical lime application to investigate how acid soils (±lime) influence the legacy effects of annual legume pastures. We measured legume and cereal growth and yield, soil-borne disease incidence, rhizosheath organic acid type and amount, legume biological nitrogen fixation (BNF) and soil moisture in Year 1, and soil microbial biomass carbon (MBC) and wheat yield and quality in Year 2. Minor differences in soil moisture and soil-borne diseases occurred between cereals and legumes, and the poor BNF contribution of all pasture legumes improved in lime treatments. Pasture legumes produced more organic acids than cereals, which increased in limed treatments. Soil MBC in Year 2 was greater following legumes than cereals. Year 2 wheat grain yield increased following pasture legumes, more so in limed treatments. The contribution of organic acid exudation by annual legume pastures to microbial community legacy effects warrants further scrutiny in semi-arid environments, particularly when acid soils limit typical rotational benefits.