This study investigates the use of project-based learning analytics as a diagnostic approach to identify gaps between administrative completion and conceptual design quality in sustainability-oriented biology teaching modules developed by pre-service biology teachers. Participants were 63 pre-service biology teachers from two classes (5A = 30 students; 5B = 33 students), who produced 13 group teaching modules. Data included project scores, formative scores, midterm and final examination scores, project-component records, questionnaire responses, and design-gap rubric scores. The data were analyzed using descriptive statistics, comparison between administrative and conceptual components, and percentage-based design-gap analysis across curriculum alignment, assessment design, digital pedagogy, deep learning, and sustainability integration. Results showed that overall student performance was relatively good and homogeneous, with a mean final score of 81.34 and a standard deviation of 2.23. However, full administrative completion of project drafts and progress reports (100.00%) did not correspond to conceptual design quality. The final teaching modules achieved only 34.90% of the target criteria for coherent integration of module components. The largest design gap was found in sustainability integration (76.90%), followed by deep learning (69.20%), assessment design (61.50%), digital pedagogy (53.80%), and curriculum alignment (46.20%). These findings indicate that project completion does not automatically ensure coherent instructional design. This study contributes by demonstrating that project-based learning analytics can reveal hidden weaknesses in sustainability-oriented instructional design that are not captured by final grades or document completion alone. The findings highlight the need for operational rubrics, formative feedback, model modules, and explicit design scaffolding.