Large duplications are a highly dynamic class of mutation; they arise, and are subsequently lost, at rates far exceeding those typically observed for single nucleotide polymorphisms (SNPs). The transient nature of large duplications means that their contribution to evolution is often overlooked. Here, we dissect the dynamics of adaptive, but unstable, large-scale duplications in evolving populations of the bacterium Pseudomonas fluorescens SBW25.We serially transfer eight replicate lines, each founded by a slow-growing P. fluorescens SBW25 mutant lacking one or more tRNA genes, for 100 days (~750 generations). We use population-level whole genome re-sequencing to show that adaptation occurs via large-scale, tandem duplications within the SBW25 chromosome. Initially, the duplications are up to ~0.9 Mb in size, and encompass many hundreds of genes. Over the course of the experiment, progressively smaller (and hence fitter and more stable) duplication fragments arise and sweep through the evolving populations. In one replicate line, a duplication fragment of just 236 bp – containing only the compensatory tRNA gene – reaches high frequency by the end of the experiment. Further, our results suggest that duplication fragment instability plays a pivotal role in the observed evolutionary process; duplication loss typically leaves no trace of the duplication fragment, regenerating the founding genotype and repeatedly providing a clean slate for the emergence of new mutations. Over time, lower-rate but higher-effect (and more stable) mutations ultimately arise and prevail in the evolving populations. Our results show that large duplications can rapidly generate an unexpected degree of diversity in bacterial genome content, with the potential to influence evolutionary outcomes.