Understanding the responses of biological communities to elevated CO₂ (eCO₂) is a central issue in ecology and global change biology, but its impacts on the diversity, composition, structure, function, and dynamics of soil microbial communities remain elusive. Also, most studies are largely based on individual free air CO₂ enrichment (FACE) experimental ecosystems, and no common patterns have emerged. Here, we first examined microbial responses to eCO₂ among six FACE sites/ecosystems using a comprehensive functional gene microarray (GeoChip 3.0), and then focused on details of metagenome sequencing analysis in one particular site. Both ecosystem and CO₂ significantly (p < 0.05) affected the functional composition, structure and metabolic potential of soil microbial communities with ecosystem having much greater influence (~47%) than CO₂ (~1.3%) or CO₂ and ecosystem (~4.1%). On one hand, microbial responses to eCO₂ shared some common patterns among different ecosystems, such as increased abundances for key functional genes involved in nitrogen fixation, carbon fixation and degradation, and denitrification. On the other hand, more ecosystem-specific microbial responses were identified in each individual ecosystem. Such changes in the soil microbial community structure were closely correlated with geographic distance, soil NO₃-N, NH₄-N and C/N ratio. Further metagenome sequencing analysis of soil microbial communities in one particular site showed eCO₂ altered the overall structure of soil microbial communities with ambient CO₂ samples retained a higher functional gene diversity than eCO₂ samples. Also the taxonomic diversity of functional genes decreased at eCO₂. Additionally, amplicon sequencing of several genes (e.g., 16S rRNA, 28S rRNA, nifH, amoA) verified the results observed above. Taken all together, this study indicates that eCO₂ may decrease the overall functional and taxonomic diversity of soil microbial communities, but such effects appeared to be ecosystem-specific, which makes it more challenging for globally or regionally predicting the responses of terrestrial ecosystems to eCO₂.