Attaining coherence in writing remains a huge challenge for English as Foreign Language (EFL) learners. This study investigated how EFL college students structured their expository essays and attained coherence in a content-based language learning course by comparing the effects of the cognitive and linguistic approaches. Three classes participated, each of which was introduced to a scaffold: linguistic Theme-Rheme (TR), an approach to examine text structure, cognitive concept mapping (CM), tools to structure content knowledge, and a traditional approach for the control group. Pre- and post-knowledge tests and post-intervention essays were collected. The results showed that prior knowledge and different organization strategies played different roles in predicting overall writing scores and, specifically, the organization scores. Generally, a wider range of organization features predicted CM group's essays. Among the organization features, linear thematic progression, often contributing to effective flow, consistently predicted both overall writing and organization scores in the combined samples, and had the strongest predictive power in the TR group. By contrast, none of the organization features was found to significantly predict the control group's writing performance. The results suggest that the two experimental approaches have different potentials in developing different organization strategies in attaining coherence in writing.