Reviewers rarely comment on the same aspects of a manuscript, making it difficult to properly assess manuscripts' quality and the quality of the peer review process. The goal of this pilot study was to evaluate structured peer review implementation by: 1) exploring whether and how reviewers answered structured peer review questions, 2) analysing reviewer agreement, 3) comparing that agreement to agreement before implementation of structured peer review, and 4) further enhancing the piloted set of structured peer review questions. Structured peer review consisting of nine questions was piloted in August 2022 in 220 Elsevier journals. We randomly selected 10% of these journals across all fields and IF quartiles and included manuscripts that received two review reports in the first 2 months of the pilot, leaving us with 107 manuscripts belonging to 23 journals. Eight questions had open-ended fields, while the ninth question (on language editing) had only a yes/no option. The reviews could also leave Comments-to-Author and Comments-to-Editor. Answers were independently analysed by two raters, using qualitative methods. Almost all the reviewers (n = 196, 92%) provided answers to all questions even though these questions were not mandatory in the system. The longest answer (Md 27 words, IQR 11 to 68) was for reporting methods with sufficient details for replicability or reproducibility. The reviewers had the highest (partial) agreement (of 72%) for assessing the flow and structure of the manuscript, and the lowest (of 53%) for assessing whether interpretation of the results was supported by data, and for assessing whether the statistical analyses were appropriate and reported in sufficient detail (52%). Two thirds of the reviewers (n = 145, 68%) filled out the Comments-to-Author section, of which 105 (49%) resembled traditional peer review reports. These reports contained a Md of 4 (IQR 3 to 5) topics covered by the structured questions. Absolute agreement regarding final recommendations (exact match of recommendation choice) was 41%, which was higher than what those journals had in the period from 2019 to 2021 (31% agreement, P = 0.0275). Our preliminary results indicate that reviewers successfully adapted to the new review format, and that they covered more topics than in their traditional reports. Individual question analysis indicated the greatest disagreement regarding the interpretation of the results and the conducting and the reporting of statistical analyses. While structured peer review did lead to improvement in reviewer final recommendation agreements, this was not a randomized trial, and further studies should be performed to corroborate this. Further research is also needed to determine whether structured peer review leads to greater knowledge transfer or better improvement of manuscripts.