Ecosystems comprise flows of energy and materials, structured by organisms and their interactions. Important generalizations have emerged in recent decades about conversions by organisms of energy (metabolic theory of ecology) and materials (ecological stoichiometry). However, these new insights leave a key question about ecosystems inadequately addressed: are there basic organizational principles that explain how the interaction structure among species in ecosystems arises? Here we integrate recent contributions to the understanding of how ecosystem organization emerges through ecological autocatalysis (EA), in which species mutually benefit through self-reinforcing circular interaction structures. We seek to generalize the concept of EA by integrating principles from community and ecosystem ecology. We discuss evidence suggesting that ecological autocatalysis is facilitated by resource competition and natural selection, both central principles in community ecology. Furthermore, we suggest that pre-emptive resource competition by consumers and plant resource diversity drive the emergence of autocatalytic loops at the ecosystem level. Subsequently, we describe how interactions between such autocatalytic loops can explain pattern and processes observed at the ecosystem scale, and summarize efforts to model different aspect of the phenomenon. We conclude that EA is a central principle that forms the backbone of the organization in systems ecology, analogous to autocatalytic loops in systems chemistry.