Nitrogen (N) deposition is a chronic disturbance in many semi-arid shrublands; however, variations in soil carbon (C) availability and quality occur over shorter time scales associated with seasonal changes in plant growth and mortality. Variations in N and C availability can alter soil microbial community structure and function, which can feed back on a variety of ecosystem processes. Here we conducted a laboratory experiment where soil collected from chaparral and coastal sage scrub (CSS) ecosystems exposed to experimental N addition for over 17 years was subjected to pulses of labile (glucose) or recalcitrant (lignin) C. We used amplicon (16S rRNA) sequencing to quantify bacterial relative abundance and diversity, and measured microbial respiration and extracellular enzyme activity to evaluate how rates of microbial activity were affected by changes in N and C availability and C quality. We predicted that (1) C inputs would cause a change in the relative abundance of bacterial taxa and increase microbial biomass and rates of activity, (2) responses to glucose would be greater than lignin, and (3) that microbial responses would be highest in the N + glucose treatment. Our data partially supported these hypotheses. Relative abundance of taxa such as Actinobacteria, Saccharibacteria, Gemmatimonadetes, and Chloroflexi were significantly affected by long-term N addition, while others such as Proteobacteria, Bacteroidetes, and Firmicutes responded to C pulses or combinations of C and N inputs, but the response often depended on vegetation type or season. For most of these taxa, pulses of readily available glucose caused an increase in relative abundance except Proteobacteria, which had the largest increase in lignin treatments. Changes in relative abundance caused shifts in alpha- and beta-diversity, but these shifts were contingent on season (fall vs. spring) and whether soils were subjected to N addition. Microbial biomass and rates of respiration were significantly higher in glucose treatments and depressed in soils exposed to N; however, rates of potential beta-glucosidase, N-acetyl-glucosaminidase (NAGase), and peroxidase activity were often highest in soils treated with lignin, which presumably reflects the microbial community's adaptation to woody C inputs associated with these shrublands. Our results often revealed significant interactions between C and N on microbial community structure and function, indicating that changes in C quantity and quality, that often accompany long-term N deposition, will interact with N availability to alter microbial communities in these semi-arid shrublands.