Assessing progress towards environmental sustainability requires a robust and systematic knowledge base. Economy-wide material flow accounting (ew-MFA) is an established method to monitor resource use across scales and its headline indicators are widely used in policy. However, ew-MFA is currently limited by its empirical focus on annual flows of material and energy, because it neglects the pivotal role of in-use material stocks of manufactured capital. Explicitly integrating in-use stocks enables new insights into a range of Ecological Economics' topics, such as the biophysical assessment of socio-economic systems, the circular economy and stock-flow consistent scenarios. Herein, we conceptually and practically expand the ew-MFA framework towards jointly addressing material flows, in-use stocks of manufactured capital and waste, using a fully consistent dynamic model of Material Inputs, Stocks and Outputs (MISO-model). We review the stock modelling literature, propose a novel distinction of stock-driven versus inflow-driven approaches and situate the MISO-model as the latter. We then investigate the global dynamics of socio-metabolic flows and in-use stocks from 1900 to 2014, explore model sensitivities and quantify and attribute uncertainty. Two exemplary scenarios are presented. Through these innovations for ew-MFA, we enable a dynamic and comprehensive assessment of resource use, stocks and all wastes in the socio-economic metabolism.