The extracellular matrix (ECM) is a master regulator of cellular phenotype and behaviour. It plays a critical role in both normal tissue homeostasis and pathological disease progression. Here we present a fast and efficient approach (ISDoT), whereby whole organs, or entire organisms, can be decellularised leaving their native ECM architecture intact. We demonstrate how these 3D decellularised tissues can be used for high-resolution fluorescence and second harmonic imaging, as well as quantitative proteomic interrogation of the ECM. We show that our method is superior to other existing methods in its ability to preserve the structural integrity of the ECM, facilitate high-resolution imaging and quantitatively detect ECM proteins. We provide the first detailed high-resolution sub-micron imaging of ECM topography at the cancer metastatic niche, and perform detailed imaging of interstitial and vessel ECM changes in tumour, adjacent and metastatic tissues. We therefore demonstrate that our method can be used to study native ECM structure under normal and pathological conditions in unprecedented detail.