The current study focused on scaffolding programmes, including cognitive and meta-cognitive components, for science problem solving in a computerised learning environment to identify their unique effects on aspects of student motivation. Using expectancy-value theory as a conceptual framework, the current study focused on two motivational aspects: intrinsic value and perceived cost. Four scaffolding components were identified (structural, reflective, subject matter and enrichment) and used in different configurations to construct four scaffolding programmes ranging from low support (Enrichment) to partial support (Operative and Strategic) to full support (Integrated). The participants were seventh-grade students (N = 458) sampled from 15 different classes in 3 middle schools. The classes were randomly assigned to the five treatment groups (four 'scaffolding programmes' and one control). The intervention was conducted over approximately 6 months as part of the regular class curriculum. The first phase of the study was based on self-report surveys distributed twice to all participants, and the second phase was based on observations of a sub-sample (N = 145). The findings indicated that the integrated group demonstrated the most adaptive patterns of motivation. Specifically, the integrated group was the only group that showed no decline in intrinsic value or increases in perceived cost. Both the strategic and integrated groups had higher levels of observed willingness to invest effort and reports of intentional learning when using the scaffolding software. The common feature of these groups is the reflection component, which implies that reflection and its combination with subject matter have positive effects on motivation.