Major educational policy groups call on learners to engage in inquiry-based activities. With a growing amount of information now available online, there is an increased focus on online inquiry where learners ask research questions; search digital libraries and other information sources; and read, assess, and synthesize that information. Metacognitive skills are important for engaging in complex practices like online inquiry, but those skills are weak in novice learners. In this article, we propose a framework that describes the types of metacognitive problems that learners exhibit during online inquiry and the ways that software can serve a scaffolding function to address those problems and support learners through those metacognitive issues. Specifically, we consider how three categories of metacognition relate to online inquiry--task understanding and planning, monitoring and regulation, and reflection--and the issues learners face within each. Our framework describes different types of scaffolding features from a range of software tools that can support learners with the identified metacognitive issues in different ways, such as by describing online inquiry task structures for better task understanding, making planning an explicit activity, helping learners see online inquiry task spaces and strategies to monitor and regulate work, and describing to learners the important aspects of online inquiry that they should reflect on during their work. A common thread with these scaffolding features is the fact that they make different aspects of metacognition, which tends to be implicit to learners, more explicit so learners can engage in the metacognitive activity that they otherwise tend to bypass.