South Africa scored worst in scientific achievement at the night-grade level in the Trends in International Mathematics and Science Studies (TIMSS) 2019. Singapore, the TIMSS 2019 leader, and South Africa are compared. Quantitative positivist design was applied. Multi-level models showed that, for both counties, learners with a higher sense of belonging performed better. In Singapore, school buildings, grounds, and audio-visual tools for instruction were significant predictors; however, in South Africa, appropriate instructional materials and technologically skilled staff were. Singaporean learners at schools where principals claimed their audio-visual resources for instruction were not affected by shortage or inadequacy performed significantly worse than those in schools where principals said it is affected. Several explanations were offered for this surprising discovery, but Singapore education officials and stakeholders may need to investigate more. Thus, for Singapore, we urge additional investigation of the surprising outcome while, for South Africa, prioritising schools with insufficient instructional materials and training all teachers in technology. Stakeholders should also invest in school climate surveys and other interventions supporting a healthy school environment. Additional research is encouraged to establish the nature of the impact that a healthy school climate has on learner achievement through longitudinal studies where causation can be proven.