Powerful arguments have been made recently to advocate for the introduction of systems thinking in chemistry education to equip graduates to address sustainability challenges. This contribution describes systems thinking activities and an assessment tool that enables meaningful learning in first-year organic chemistry as students engage with the molecular-level foundation and real-world implications of the system under consideration. The activity incorporates concept maps and systems-oriented concept mapping extensions (SOCMEs) as visualization tools to scaffold the development of systems thinking skills. A rubric based on the SOLO taxonomy was designed and used to assess evidence of systems thinking skills demonstrated on SOCMEs. The activity was implemented in a small and a large group of 18 and 219 participants respectively, where findings from both groups are presented. The grading of six SOCMEs by three independent raters proved to be inconsistent at higher thinking SOLO levels, where rater experience was flagged as an area for future improvement to ensure raters are proficient in assessing systems thinking. However, meaningful progress was made to assess the quality of learning. The rubric was an effective tool for formative and low-stakes assessment to drive the teaching and learning of systems thinking in chemistry.