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Abstract Background Process skills such as critical thinking and information processing are commonly stated outcomes for STEM undergraduate degree programs, but instructors often do not explicitly assess these skills in their courses. Students are more likely to develop these crucial skills if there is constructive alignment between an instructor’s intended learning outcomes, the tasks that the instructor and students perform, and the assessment tools that the instructor uses. Rubrics for each process skill can enhance this alignment by creating a shared understanding of process skills between instructors and students. Rubrics can also enable instructors to reflect on their teaching practices with regard to developing their students’ process skills and facilitating feedback to students to identify areas for improvement. Results Here, we provide rubrics that can be used to assess critical thinking and information processing in STEM undergraduate classrooms and to provide students with formative feedback. As part of the Enhancing Learning by Improving Process Skills in STEM (ELIPSS) Project, rubrics were developed to assess these two skills in STEM undergraduate students’ written work. The rubrics were implemented in multiple STEM disciplines, class sizes, course levels, and institution types to ensure they were practical for everyday classroom use. Instructors reported via surveys that the rubrics supported assessment of students’ written work in multiple STEM learning environments. Graduate teaching assistants also indicated that they could effectively use the rubrics to assess student work and that the rubrics clarified the instructor’s expectations for how they should assess students. Students reported that they understood the content of the rubrics and could use the feedback provided by the rubric to change their future performance. Conclusion The ELIPSS rubrics allowed instructors to explicitly assess the critical thinking and information processing skills that they wanted their students to develop in their courses. The instructors were able to clarify their expectations for both their teaching assistants and students and provide consistent feedback to students about their performance. Supporting the adoption of active-learning pedagogies should also include changes to assessment strategies to measure the skills that are developed as students engage in more meaningful learning experiences. Tools such as the ELIPSS rubrics provide a resource for instructors to better align assessments with intended learning outcomes.