This manual presents the objectives and procedures for application of a research framework using a mixed-methods approach from the Education Resilience Approaches (ERA) Program to help collect evidence on the opportunities, support, and process that help children and youth succeed in school in spite of overwhelmingly difficult contexts. The Resilience in Education Systems Research (RES-Research) manual provides guidance across the research process, positioning and conceptualizing, designing, data collection and analysis for resilience-focused studies. It emphasizes a mixed-methods approach to sampling, data collection and analysis to tap into the benefits of integrating diverse research approaches. The RES-Research guide supports studies to inform discussion across education actors, such as policy makers, ministry officials, other service providers, and education institutions, on how schools, universities, and education systems can collaborate to understand adversity, recognize the assets and opportunities for personal, group and social transformations, and inform policy makers, program designers, and service providers on context- and situation-relevant approaches to foster resilience as well as mitigate the sources of adversity.