This paper begins by raising concerns about the impact of technologies such as ChatGPT on students’ writing, particularly their reduced learner autonomy and superficial engagement with the content. While standalone chat-based large language models (LLMs) often produce suboptimal writing output, there is evidence that purpose-built AI writing assistance tools can enhance the writing process. This study investigates how different AI-assisted approaches affect writers’ sense of autonomy and the depth of their knowledge transfer. In a randomized controlled trial of 90 undergraduate students, we compared three conditions: a chat-based LLM writing assistance tool, an integrated AI writing assistance tool that supported multiple sub-courses, and a standard writing interface (control). Among the AI-assisted conditions, we found that students who used the integrated AI writing assistance tool reported greater autonomy over the writing process and engaged in deeper knowledge transfer overall. These results suggest that thoughtfully designed AI writing assistance targeting specific aspects of the writing process can help students improve their engagement with the content while maintaining ownership of their work.