Ecological economics is largely about the ‘substantive’ (in ‘kind’) study of the economy, as opposed to a purely ‘formal’ economic analysis (in ‘money’). Following Kapp, Polanyi and others, this article argues that ‘substantive economics’ is interested in the biophysical and politico-institutional structure of the economy rather than in correct prices within a particular axiomatic conformity, as in ‘formal economics’. After outlining the history of the substantive vs. formal dichotomy, we point out that socio-metabolic analyses are ecological economics' most significant contribution towards substantive economics. The core of this article then compares what could be today's two best candidates for offering a distinctive foundation to ecological economics as substantive economics: Material and Energy Flows Analyses (MEFA) and Multi-Scale Integrated Analyses of Societal and Ecosystem Metabolism (MuSIASEM). While MEFA is more easily comparative and historical, MuSIASEM is more integrative and comprehensive. Yet we also argue that socio-metabolic analyses represent one of the three pillars of substantive economics and that both MEFA and MuSIASEM are still weak in integrating the politico-institutional structure (second pillar) and a theory of needs (third pillar). If such an integration was done, ecological economics would be in a position to offer a full-fledge, alternative ‘substantive economic theory’.