The ability to design and interpret controlled experiments is an important scientific process skill and a common objective of science standards. Numerous intervention studies have investigated how the control-of-variables-strategy (CVS) can be introduced to students. However, a meta-analysis of 72 intervention studies found that the opportunity to train CVS skills with hands-on tasks (g = 0.59) did not lead to better acquisition of CVS relative to interventions without a hands-on component (g = 0.74). We conducted an intervention study in which we investigated the differential effects of hands-on and paper-and-pencil training tasks on 161 eighth-grade students’ achievement. CVS was demonstrated to all students before they were grouped into a hands-on or a paper-and-pencil training condition. In both training conditions, students designed and interpreted experiments about which variables influence the force of electromagnets. Students in the hands-on group interacted with physical equipment while students in the paper-and-pencil group planned experiments using sketches and interpreted the outcome of experiments presented in photographs. We found no general advantage or disadvantage of hands-on tasks, as both groups did equally well on CVS and content knowledge tests. However, hands-on students outperformed paper-and-pencil students on a hands-on test identical to the training tasks, whereas the paper-and-pencil students outperformed hands-on students on a science fair poster evaluation task similar to the paper-and-pencil training. In summary, students learned task-specific procedural knowledge, but they did not acquire a deeper conceptual understanding of CVS or the content domain as a function of type of training. Implications for instruction and assessment are discussed.