The integrated nature of the Sustainable Development Goals (SDGs) presents a challenge to implementing the 2030 Agenda. Analytical methods to support decision-makers are often developed without explicitly incorporating decision-makers’ views and experience. Here, we investigate whether existing methods are fit-for-purpose in supporting decision-makers at national and subnational levels. We identify prominent methods for SDG interaction analysis, which we then evaluate by engaging directly (via a survey and interviews) with method developers and decision-makers in Sweden. We find that decision-makers prioritize methods that are simple and flexible to apply and able to provide directly actionable and understandable results. They are less concerned with the accuracy, precision, completeness or quantitative nature of the knowledge. Prominent categories of methods include self-assessment, expert judgement, literature-based, statistical analyses and modelling. Interviewed decision-makers consider these methods in line with the features prioritized in the survey but highlight low performance on features they value highly, such as the extent to which results are actionable and overall ease of use. Methods developers have limited awareness of decision-makers’ priorities and requirements, so hindering methodological advancement. They should focus on the practical value of applications to support decision-makers, resource-constrained organizations and those seeking to evaluate multiple cases.