Background School food outlets represent a key setting for public health nutrition intervention. The recent proliferation of web-based food ordering systems provides a unique opportunity to support healthy purchasing from schools. Embedding evidence-based choice architecture strategies within these routinely used systems provides the opportunity to impact the purchasing decisions of many users simultaneously and warrants investigation. Objective This study aims to assess the effectiveness of a multistrategy behavioral intervention implemented via a web-based school canteen lunch ordering system in reducing the energy, saturated fat, sugar, and sodium content of primary students’ web-based lunch orders. Methods The study used a parallel-group, cohort, cluster randomized controlled trial design with 2207 students from 17 Australian primary schools. Schools with a web-based canteen lunch ordering system were randomly assigned to receive either a multistrategy behavioral intervention that included choice architecture strategies embedded in the web-based system (n=9 schools) or the standard web-based ordering system only (n=8 control schools). Automatically collected student purchasing data at baseline (term 2, 2018) and 12 months later (term 2, 2019) were used to assess trial outcomes. Primary trial outcomes included the mean energy (kJ), saturated fat (g), sugar (g), and sodium (mg) content of student lunch orders. Secondary outcomes included the proportion of all web-based lunch order items classified as everyday, occasional, and caution (based on the New South Wales Healthy School Canteen Strategy) and canteen revenue. Results From baseline to follow-up, the intervention lunch orders had significantly lower energy content (−69.4 kJ, 95% CI −119.6 to −19.1; P=.01) and saturated fat content (−0.6 g, 95% CI −0.9 to −0.4; P<.001) than the control lunch orders, but they did not have significantly lower sugar or sodium content. There was also a small significant between-group difference in the percentage of energy from saturated fat (−0.9%, 95% CI −1.4% to −0.5%; P<.001) but not in the percentage of energy from sugar (+1.1%, 95% CI 0.2% to 1.9%; P=.02). Relative to control schools, intervention schools had significantly greater odds of having everyday items purchased (odds ratio [OR] 1.7, 95% CI 1.5-2.0; P<.001), corresponding to a 9.8% increase in everyday items, and lower odds of having occasional items purchased (OR 0.7, 95% CI 0.6-0.8; P<.001), corresponding to a 7.7% decrease in occasional items); however, there was no change in the odds of having caution (least healthy) items purchased (OR 0.8, 95% CI 0.7-1.0; P=.05). Furthermore, there was no change in schools’ revenue between groups. Conclusions Given the evidence of small statistically significant improvements in the energy and saturated fat content, acceptability, and wide reach, this intervention has the potential to influence dietary choices at a population level, and further research is warranted to determine its impact when implemented at scale. Trial Registration Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12618000855224; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375075. International Registered Report Identifier (IRRID) RR2-10.1136/bmjopen-2019-030538