For decades, Ecological Economics has spent many resources on research-paradigmatic conflicts. The resulting lack of methodological alignment and consistency creates transaction cost, divides the research community and undermines the paradigmatic agreement needed in working on shared goals. Building on a multivariate statistical full-text analysis of all empirical research papers published in the journal Ecological Economics in the period 1989–2021 (N = 3972), we empirically investigate the landscape of research methods used in the journal Ecological Economics. Our statistical results support the existence of five different methodological clusters. We argue that sustaining pluralism without fragmentation requires context-dependent choices of methods, supported by a diversification of Ecological Economics orientational paradigms. Methods should be understood as means rather than ends, valued for their ability to address questions aligned with the field's pre-analytical vision.