Interactions with the extracellular matrix (ECM) dictate cell fates. However, the complexity of dense ECM network and cell-surface molecules prevent the study of their dynamic interaction at the molecular level on living cells. Here, we focus on peptidyl prolyl cis/trans isomerases (PPIases) to dissect prolyl isomerization from other dynamic events. We reveal the contribution of PPIase on the mechanical properties of various ECM materials and on the dynamic cell–ECM interaction. To avoid complications associated with the existing spectroscopy-based methods such as light scattering, an assay was developed for detecting PPIase activity on living cell surface. This assay allows us to correlate PPIase activity with ECM development, and with the physiological and pathological states of the cells, including the functional properties of cancer cells and immune effector cells.