Large-scale DNA deletions and gene loss are pervasive in bacterial genomes. This observation raises the possibility that evolutionary adaptation has altered bacterial genome organization to increase its robustness to large-scale tandem gene deletions. To find out, we systematically analyzed 55 bacterial genome-scale metabolisms and showed that metabolic gene ordering renders an organism's viability in multiple nutrient environments significantly more robust against tandem multigene deletions than expected by chance. This excess robustness is caused by multiple factors, which include the clustering of essential metabolic genes, a greater-than-expected distance of synthetically lethal metabolic gene pairs, and the clustering of nonessential metabolic genes. By computationally creating minimal genomes, we show that a nonadaptive origin of such clustering could in principle arise as a passive byproduct of bacterial genome growth. However, because genome randomization forces such as translocation and inversion would eventually erode such clustering, adaptive processes are necessary to sustain it. We provide evidence suggesting that this organization might result from adaptation to ongoing gene deletions, and from selective advantages associated with coregulating functionally related genes. Horizontal gene transfer in the presence of gene deletions contributes to sustaining the clustering of essential genes. In sum, our observations suggest that the genome organization of bacteria is driven by adaptive processes that provide phenotypic robustness in response to large-scale gene deletions. This robustness may be especially important for bacterial populations that take advantage of gene loss to adapt to new environments.