Single-cell DNA sequencing complements the metagenomic analysis of uncultured bacteria by revealing cell-to-cell variation, linking host genomes to extrachromosomal DNA, and providing strain-level taxonomic resolution. However, current techniques are limited to processing fewer than 1,000 cells and produce single-amplified genomes (SAGs) of low completeness due to biases in whole genome amplification (WGA). We present an innovative, cost-effective approach to sequence up to 10,000 SAGs with superior genome recovery. Individual microbial cells are isolated into 70 µm semi-permeable capsules (SPCs), enabling compartmentalized multi-step processing - including lysis, WGA, and barcoding - of all cells simultaneously at a cost of less than $1 per cell. Using well-characterized E. coli and B. subtilis, we demonstrate >90% genome recovery per SAG at sequencing depths below 10x and <1% cross-contamination. Additionally, we processed a commercially available microbial community standard and were able to detect all species within the mixture. The advantages of SAG sequencing are especially valuable for uncovering the diversity and unique adaptations in the context of microbial ecology. We processed soil and aquatic samples to generate matched SAG and MAG datasets, with the latter obtained through bulk metagenomics. SAG assemblies produced longer contigs and revealed detailed genomic features, most notably the linkage between viral and plasmid sequences and their hosts. The linkage information was lost in the MAG dataset. Our high-throughput SAG sequencing workflow provides a detailed view of microbial communities, offering unmatched resolution and scalability. This capsule-based single-cell sequencing technology opens new horizons for microbial genomics research.