The mechanical properties of bacterial biofilms depend on the composition and microstructure of their extracellular matrix (ECM), which constitutes a network of extracellular proteins and polysaccharide fibers. In particular, Escherichia coli macrocolony biofilms were suggested to present tissue-like elasticity due to a dense fiber network consisting of amyloid curli and phosphoethanolamine-modified cellulose (pEtN-cellulose). To understand the contribution of these two main ECM components to the emergent mechanical properties of E. coli biofilms, we performed shear-rheology and microindentation experiments on biofilms grown from E. coli strains that produce different ECM. We measured that biofilms containing curli fibers are stiffer in compression than curli-deficient biofilms. We further quantitatively demonstrate the crucial contribution of pEtN-cellulose, and especially of the pEtN modification, to the stiffness and structural stability of biofilms when associated with curli fibers. To compare the differences observed between the two methods, we also investigated how the structure and mechanical properties of biofilms with different ECM compositions are affected by the sample preparation method used for shear-rheology. We found that biofilm homogenization, used prior to shear-rheology, destroys the macroscale structure of the biofilm while the microscopic ECM architecture may remain intact. The resulting changes in biofilm mechanical properties highlight the respective advantages and limitations of the two complementary mechanical characterization techniques in the context of biofilm research. As such, our work does not only describe the role of the ECM on the mechanical properties of E. coli biofilms. It also informs the biofilm community on considering sample preparation when interpreting mechanical data of biofilm-based materials.