The biomechanical properties of the extracellular matrix (ECM) play an important role in cell migration, gene expression, and differentiation. Biomechanics measurements of ECM are usually performed on cryotomed tissue sections. However, studies on cell/matrix interplay are impossible to perform due to disruptions in cell viability and tissue architecture from freeze-thaw cycling. We developed a technique to map the stiffness of living cells and surrounding matrix by atomic force microscopy and use fluorescence microscopy to relate those properties to changes in matrix and cell structure in embryonic and adult tissues in situ. Stiffness mapping revealed significant differences between vibratomed (living) and cryotomed tissues. Isolated cells are softer than those in native matrix, suggesting that cell mechanics are profoundly influenced by their three-dimensional environment and processing state. Viable tissues treated by hyaluronidase and cytochalasin D displayed targeted disruption of matrix and cytoskeletal networks, respectively. While matrix stiffness affected cellular stiffness, changes in cell mechanics did not reciprocally influence matrix stiffness.