Intrinsic motivation plays a unique mediating role in student academic performance. An inquiry-based learning (IBL) physics practical is studied in terms of effects on secondary school students' intrinsic motivation towards performing science practicals. After performing IBL experiments on ionizing radiation, 38 secondary school physics students were interviewed and expressed their need for support in two main areas: the inquiry process and non-salient tasks, i.e., operating the equipment. The IBL experiments were revised accordingly, providing scaffolding through revised worksheets and videos on the use of the equipment. Subsequently, a quasi-experiment was carried out. One experimental group received both a revised worksheet and a video (N = 88), the other only received the worksheet (N = 67). Students performing the same practical on the basis of a step-by-step instruction sheet were used as a control group (N = 87). Five subscales of the intrinsic motivation inventory were used as a pre- and post-test for all three groups. Results show significant gains in the Interest/Enjoyment as well as Effort/Importance subscales favouring both IBL groups. With an instructional video, all five subscales show a significant increase as compared to the control group. The results point to the advantages of using an IBL approach for practicals, provided appropriate scaffolding is used in terms of equipment operation and inquiry process.