Data for research published as https://doi.org/10.1101/2023.12.10.570986 and currently under review for publication in peer reviewed journal, with data here grouped by main figures as in the submitted manuscript.Complement proteins eliminate Gram-negative bacteria in the blood via the formation of membrane attack complex (MAC) pores in the outer membrane. However, it remains unclear how outer membrane poration leads to inner membrane permeation and cell lysis. Using atomic force microscopy (AFM) on living Escherichia coli (E. coli), we probed MAC-induced changes in the cell envelope and correlated these with subsequent cell death. Initially, bacteria survived despite the formation of hundreds of MACs randomly distributed over the cell surface. This was followed by larger-scale disruption of the outer membrane, including propagating defects and fractures, and by an overall swelling and stiffening of the bacterial surface, which precede inner membrane permeation. We conclude that bacterial cell lysis is only an indirect effect of MAC formation; outer membrane poration leads to mechanical destabilization of the cell envelope, reducing its ability to contain the turgor pressure, leading to inner membrane permeation and cell death.The data stored here include AFM data of living E. coli cells exposed to complement proteins and particularly the membrane attack complex; results of data processing in the form of background subtracted images and mechanical data; and brightfield and fluorescence microscopy images that were taken complementary to AFM data on the same cells.Data files can be open with open-source AFM image processing software (e.g., Gwyddion), general image viewers (e.g., for jpeg, tiff, pdf) or any spreadsheet text readers (for e.g. txt and csv files).