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The systematic collection, analysis, and interpretation of antimicrobial resistance (AMR) data are imperative to quantify the AMR burden, monitor and identify emerging AMR, and inform global, international, and national health strategies and guidelines. Despite ongoing global efforts to improve surveillance capacities across Nigeria and other African countries, laboratory information management systems (LIMS) that could improve data quality, and completeness remain underutilized. We used a participatory research approach, drawing on the unique experiences of various stakeholders, such as data analysts, laboratory scientists, infection prevention and control specialists, medical doctors, and representatives from the National Coordinating Center in Nigeria. Over two phases of evidence synthesis, involving in-depth interviews and a participatory co-design workshop, we sought to understand the experiences of key stakeholders in using the LIMS tool, WHONET, for AMR surveillance, and co-develop solutions and priorities to address the challenges they experience. We identified a complex interplay of systemic/political factors and structural/user-related factors that influence the use of WHONET as a LIMS. Key areas for intervention identified by stakeholders include addressing infrastructural deficits, enhancing stakeholder engagement, and improving the perceived usefulness of the system, as well as the need for management support. Stakeholders also identified 18 potential solutions to tackle key challenges, ten of which require low effort and have a high influence on LIMS use behaviors. Our study highlights the multifaceted challenges affecting the effective utilization of WHONET for AMR surveillance in Nigeria. The co-developed solutions provide a roadmap for targeted interventions to strengthen AMR surveillance capacity and inform evidence-based public health strategies.