Hydrogels are widely used as mimics of the native extracellular matrix as their physical and biological properties can be tuned over a wide range to match those of the native tissue. Cells encapsulated within hydrogels have recently been reported to modify their local surroundings by secreting and assembling proteins pericellularly, which in turn impacts their fate. As a result, methods to characterise and visualise the secreted matrix are becoming increasingly important in the development of regenerative therapies and in understanding cell behaviour within 3D matrices. Here, by combining fluorescent non-canonical amino acid tagging with confocal Raman spectral imaging, we aimed to create 3D maps of human mesenchymal stromal cells (hMSC) and their secreted matrix when embedded within hydrogels. To demonstrate the value of our combined technique in a tissue engineering context, we cultured hMSC in Dopa-modified hyaluronic acid-based hydrogels and treated cultures with the 2-oxyglutarate analogue dimethyloxalyglycine (DMOG), which mimics the cellular effects of physiological hypoxia and can both promote the chondrogenic differentiation of progenitor cells and enhance cartilage-like matrix formation. Quantitative analyses of the distribution of newly synthesised proteins combined with principal components analyses of Raman spectra showed that DMOG prompted encapsulated cells to secrete more protein pericellularly than did untreated controls. Our findings demonstrate that it is possible to visualise both the 3D secreted matrix and cellular contents using simple, unbiased, inexpensive techniques, providing complementary information on cells and their secreted matrix when encapsulated within 3D hydrogels.