Data on fever and malaria cases reported by health facilities are used for tracking incidence and quantification of malaria commodity needs in Guinea. Periodic assessments of the quality of malaria case management and routine data are a critical activity for the malaria program. In May-June 2018, survey teams visited 126 health facilities in six health districts purposefully selected to represent a spectrum (Stratum 1-high, Stratum 2-intermediate, and Stratum 3-low) of perceived quality of case management and reporting, as assessed from an a priori analysis of routine data. Surveyors performed exit interviews with 939 outpatients and compared results with registry data for interviewed patients. Availability of rapid diagnostic tests (RDTs) and artemisinin-based combination therapies (ACTs) was 100% in Strata 1 and 2, compared with 82% (95% CI: 63-92%) for RDTs and 86% (68-95%) for any formulation of ACT in Stratum 3. Correct case management for suspect malaria cases was 85% in both Stratum 1 (95% CI: 78-90%) and Stratum 2 (79-89%), but only 52% (37-67%) in Stratum 3. Concordance between exit interviews and registry entries for key malaria indicators was significantly higher in Strata 1 and 2 than in Stratum 3. Both adherence to national guidelines for testing and treatment and data quality were high in Strata 1 and 2, but substandard in Stratum 3. The survey results reflected the trends seen in the routine data, suggesting that analysis of routine data can identify areas requiring more attention to improve malaria case management and reporting.