Urinary tract infections (UTIs) are one of the most prevalent bacterial infections, with Uropathogenic E. coli (UPEC) causing around 80% of all diagnosed infections of the urinary tract. During the infection cycle, UPEC undergoes striking morphology changes, where a subset of cells elongates without dividing, forming long filamentous cells that can reach several 100s of micrometres in length. Very little is known about how and why these cells adopt this morphology. We used a UTI flow model where immortalized human bladder epithelial cells were infected with UPEC, simulating various stages of the UTI infection cycle. In the final stage of the infection cycle, in the presence of urine, UPEC is fluxed out of the bladder cells, adopting filamentous morphology. To uncover potential proteins involved in filamentation, a comparative shot gun proteomic analysis was performed on UPEC cells undergoing the flow of urine or a flow of eukaryotic growth medium (as a control). We observed that 686 proteins had a significant difference in abundance, many with roles related to metabolism. uidA was increased in abundance by a log2 fold change of 12. malE and malM, proteins associated with the transport of malto-oligosaccharides, decreased in abundance by -6.15 and -5.30, respectively. There were fewer significant abundance changes in cell division proteins than expected, possibly suggesting that metabolism proteins play a greater role in filamentation than cell division proteins.