Collaboration scripts can help learners to engage in argumentation and knowledge acquisition. However, they might have differential effects for learners holding differently structured knowledge (internal scripts) on argumentation. We investigated how external scripts interact with learners' internal scripts concerning collaborative argumentation. 98 students from two secondary schools participated. Two versions of an external collaboration script (high vs. low structured) supporting argumentation were embedded within a web-based collaborative inquiry curriculum. Students' internal scripts were classified as either high or low structured, establishing a 2x2-factorial design. Results suggest that the high structured external script supported all learners, regardless of their internal scripts, concerning the acquisition of domain-general knowledge. Learners' internal scripts influenced the acquisition of domain-specific knowledge. Results from two case studies reveal differences in argumentation processes attributable to the learners' internal scripts. Results are discussed in terms of their theoretical relevance and practical implications for learning with collaboration scripts.