With highly effective diagnostic, prevention, and treatment innovations available in HIV programs globally, the HIV field is increasingly turning to implementation and service delivery questions. • Developing guidelines for implementation of interventions is markedly challenged by limitations in primary implementation research design and reporting, as well as difficulties in application of evidence synthesis and guideline development tools originally developed to appraise evidence for efficacy. • Drawing on the processes of developing the WHO HIV service delivery guidelines for testing and treatment between 2018 and 2021, we present challenges and identify areas for future methodological development to improve the incorporation of implementation research across the full spectrum of the evidence generation continuum. • We highlight gaps in design, measurement, and reporting of primary implementation research, as well as underreporting of relevant program data. • We describe how routine application of current evidence synthesis tools may not sufficiently answer implementation questions and propose that methodological tools be optimized to identify high-quality non-randomized evidence and reduce penalization for heterogeneity in meta-analysis of implementation research. • These findings serve as a blueprint for further methodological work to strengthen existing evidence synthesis and guideline development tools for HIV service delivery guidelines and for implementation research more broadly.