Inquiry-based learning can be an effective approach when students are provided with sufficient guidance. However, there is an ongoing debate among practitioners about the nature, type, and level of such guidance. This study investigated the effects on middle school students' (N = 116) conceptual knowledge and inquiry skills acquisition of providing two different levels of guidance (support or direct presentation of information related to the inquiry process) in hands-on and virtual science laboratories on the topic of electricity. The study was based on a 2 × 2 between-subjects factorial quasi-experimental design. The effects of two different levels of guidance combined with either a hands-on or a virtual laboratory were examined. Findings revealed that although the level of guidance was important for students' conceptual knowledge development, it had no significant impact on their acquisition of inquiry skills. In terms of laboratory environments, it appears that a virtual laboratory and a hands-on laboratory are equally effective for the development of middle school students' conceptual knowledge and inquiry skills.