Background The aim of this study was to characterize patterns of multimorbidity across patients and identify opportunities to strengthen the informatics capacity of learning health systems that are used to characterize multimorbidity across patients. Methods Electronic health record (EHR) data on 225,710 multimorbidity patients were extracted from the Arkansas Clinical Data Repository as a use case. Hierarchical cluster analysis identified the most frequently occurring combinations of chronic conditions within the learning health system’s captured data. Results Results revealed multimorbidity was highest among patients ages 60 to 74, Caucasians, females, and Medicare payors. The largest numbers of chronic conditions occurred in the smallest numbers of patients (i.e., 70,262 (31%) patients with two conditions, two (<1%) patients with 22 chronic conditions). The results revealed urgent needs to improve EHR systems and processes that collect and manage multimorbidity data (e.g., creating new, multimorbidity-centric data elements in EHR systems, detailed longitudinal tracking of compounding disease diagnoses). Conclusions Without additional capacity to collect and aggregate large-scale data, multimorbidity patients cannot benefit from the recent advancements in informatics (i.e., clinical data registries, emerging data standards) that are abundantly working to improve the outcomes of patients with single chronic conditions. Additionally, robust socio-technical system studies of clinical workflows are needed to assess the feasibility of integrating the collection of risk factor data elements (i.e., psycho-social, cultural, ethnic, and socioeconomic attributes of populations) into primary care encounters. These approaches to advancing learning health systems for multimorbidity could substantially reduce the constraints of current technologies, data, and data-capturing processes.