This paper presents research on middle school students working on large science projects in the Knowledge Integration Environment. The objective was to develop an exemplary program of metacognitive prompts to encourage principled knowledge integration by students working on large science projects. The research indicates that metacognitive scaffolding provided through prompts improves the quality and quantity of students' work. The two studies discussed in this paper investigate students' use of two types of metacognitive prompts: activity-focused prompts and self-monitoring prompts. Activity prompts walk students through the important steps in the activities comprising a large science project while self-monitoring prompts encourage planning for and reflection on those activities. Results indicate that metacognitive prompts have both strengths and weaknesses. Activity prompts help students finish activities but do not necessarily help the students develop an integrated understanding. Self-monitoring prompts encourage students to plan their activities, remind students to reflect on their own understanding, and improve students' likelihood of explaining and justifying the decisions they make. Possible cognitive mechanisms are proposed. Contains 16 references. Sample activities are appended. (Author/JRH)