Atmospheric nitrogen (N) deposition represents an important input of N into natural ecosystems such as semiarid shrublands of Southern California, which can receive up to 45 kg N ha−1 y−1. These N inputs will presumably alter soil microbial abundance and composition and impact ecosystem N and carbon (C) cycles. We used a 16S rRNA sequencing-based approach to characterize shifts in soil bacterial communities in chaparral and coastal sage scrub (CSS) shrublands that received annual inputs of 50 kg N ha−1 over a period of 14 years. Experimental N addition caused shifts in bacterial taxonomic composition in these shrublands. CSS exposed to N had an increase in Proteobacteria and Bacteriodetes, while N inputs to chaparral caused an increase in Bacteriodetes and Firmicutes and a decrease in Acidobacteria. Canonical correspondence analysis (CCA) indicated that extractable NH4 and/or NO3 concentrations were a strong predictor of Proteobacteria and Firmicutes (positive) and Acidobacteria and Verrucomicrobia (negative) abundance. Increases in soil pH were coincident with declines in Proteobacteria but increases in Acidobacteria, while increases in total C were positively correlated with Acidobacteria abundance. These results support the hypothesis that long-term N inputs in semi-arid shrublands promote the growth of copiotrophic taxa, such as Proteobacteria, Bacteroidetes, and Firmicutes, and inhibit the growth of oligotrophic taxa like Acidobacteria. Nitrogen addition failed to affect α-diversity at the phylum level but significantly increased α-diversity of bacterial genera, and indicator species analyses revealed more genera associated with N treatment plots (125) than control plots (91). These results imply that future increases in N deposition will alter soil microbial abundance and community composition, and in turn, affect ecosystem C and nutrient cycling in these semi-arid shrublands.