Abstract The measurement of physicochemical parameters in living cells can provide information on individual cellular organelles, helping us to understand subcellular function in health and disease. While organelle‐specific chemical probes have allowed qualitative evaluation of microenvironmental variations, the simultaneous quantification of mitochondrial local microviscosity ( η m ) and micropolarity ( ϵ m ), along with concurrent structural variations, has remained an unmet need. Herein, we describe a new multifunctional mitochondrial probe ( MMP ) for simultaneous monitoring of η m and ϵ m by fluorescence lifetime and emission intensity recordings, respectively. The MMP enables highly precise measurements of η m and ϵ m in the presence of a variety of agents perturbing cellular function, and the observed changes can also be correlated with alterations in mitochondrial network morphology and motility. This strategy represents a promising tool for the analysis of subtle changes in organellar structure.