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The effect of metacognitive scaffolding instruction on learning outcomes in a chemistry course for socio-economically deprived ninth-grade learners was investigated. A quasi-experimental pretest-posttest control group design was employed, with 107 students selected from two government-sponsored schools as a sample. For collecting data, a competency-based criterion test with a reliability coefficient of 0.86 and a validity of 0.93 was used. For analysing the data, the independent samples t-test, and 2X2 factorial design ANCOVA were applied. Results demonstrated that the experimental group learners acquired significantly higher learning outcomes than the control group learners. Furthermore, the learning outcomes were found to be independent of gender and their interaction with the instructional strategies when the pre-learning outcomes were treated as a covariate.