Effective academic writing is accessible to readers because writers follow shared conventions for organization and signal their stance on particular topics; however, few specifics are known about how middle graders might develop knowledge of and use these academic language forms and functions to signal their organization and stance in persuasive essays. This study examined how differences in organization and stance marker use was related to writing quality in 664 persuasive essays written by 176 sixth, seventh, and eighth grade students. Essays were collected in the context of a supplemental vocabulary program, transcribed and analyzed for length by researchers, scored for overall writing quality by a team of teachers, and then coded for markers of organization and stance by researchers. Multilevel modeling results reveal that two specific emergent organizational marker types (evidence markers and code glosses) have statistically significant negative relationships to quality, and the variety of stance markers used is a positive predictor of quality when an interaction with length is included in the model. Findings give insight into the ways students are using organization and stance markers and point toward these language forms and functions as potentially pedagogically-relevant and worth assessing.