Global population growth, especially in developing countries, will most likely require an increase in agricultural production, but the sustainability of this production cannot be achieved without the preservation of ecosystem functions. Therefore, farmers need to know about, and deal with, the trade-offs between agricultural productivity and ecosystem functions and services. This review aims to assess practical science-based tools that can be used to make decisions for sustainable agricultural production. We reviewed 184 articles and divided them into categories depending on whether they describe tools, practices, ecosystem services, models, or other topics. Although many studies were global in scope, the approach to analyzing and assessing trade-offs appears to vary geographically. The review showed that trade-offs between agricultural productivity and ecosystem functions are most commonly studied in Europe and Asia, while few studies have been conducted in sub-Saharan Africa. Most tools in the review addressed only one or a bundle of ecosystem services, related to water, biodiversity, or climate regulation, and were designed for different types of land use and ecosystems and applicable at different scales. More practical tools for trade-off analysis have mainly been developed and applied by development organizations with support from science. Closer collaboration between practitioners, development organizations, and scientists is suggested to foster co-development of tools useful for identifying sustainable strategies for closing the yield gap, increasing productivity and for balancing ecosystem services, building on the Sustainable Development Goal’s framework and its targets for agricultural productivity and ecosystem services for trade-off analysis. We recommend the development and fine-tuning of the identified tools to specific contexts and landscapes through innovation platforms bringing together farmers, extension workers, scientists, and local decision-makers.