Crop management practices can affect the soil microbial community, but it is not clear whether the effect of these practices is measurable at the wheat root–soil interface, where the plant exerts significant influence through root exudation. In this study, wheat plants were grown in soil amended with milled canola, lucerne, lupin, pea, and wheat residues with and without lime, to determine what changes occur to microbial community structure in the rhizosphere. Rhizosphere soil collected from wheat plants at the 5-leaf stage was assessed for overall microbial functional diversity using BIOLOG analysis and the diversity of the functional gene nifH using the polymerase chain reaction (PCR), terminal restriction fragment length polymorphism (T-RFLP), and cloning. Plant development was reduced in all residue amendments except lucerne, and a high positive correlation in the non-limited treatments between plant residue nitrogen (N) content and wheat shoot N suggested microbial competition for available N. Results from BIOLOG analysis indicated significant differences in rhizosphere microbial community structure due to lime, and to a lesser extent, residue type. Diversity, measured by the Shannon Diversity Index, was higher in limed rhizosphere soil, in addition to an increase in soils amended with lucerne, lupin, and pea residues compared with amendment with wheat, canola, and control soil. Each residue amendment promoted unique microbial communities determined by multi-dimensional scaling (MDS) and analysis of similarities (ANOSIM) of the BIOLOG data; the strongest effect was produced by addition of canola residues. N-fixing bacteria were also affected by lime, but residue effects were less apparent, especially between limed samples. The factor that correlated best with both BIOLOG and nifH T-RFLP data in non-limed soil was a combination of residue sodium (Na), copper (Cu), and manganese (Mn). In limed soil, phosphorus (P), calcium (Ca), and pH correlated well with BIOLOG data, and N, potassium (K), and iron (Fe) correlated with nifH T-RFLP data. A clone library of nifH sequences from control and limed, pea-amended soils revealed significant diversity amongst nifH sequences, most clustering with α-proteobacteria, and in some instances with Geobacter sulfurreducens. Clone distribution was significantly different for control soil and pea/lime soil, especially amongst the α-proteobacteria. The results suggest that rhizosphere microorganisms can be influenced by soil amendments, and change, depending on the type of residue applied. The addition of lime, however, produced the most significant changes in microbial community structure and nifH-containing rhizobacteria, highlighting the significant functional changes that occur when soil pH is increased.