Clinical documentation improvement programs are utilized by most health care systems to enhance provider documentation. Suggestions are sent to providers in a variety of ways, and are commonly referred to as coding queries. Responding to these coding queries can require significant provider time and do not often align with workflows. To enhance provider documentation in a more consistent manner without creating undue burden, alternative strategies are required. The aim of this study is to evaluate the impact of a real-time documentation assistance tool, named AutoDx, on the volume of coding queries and encounter-level outcome metrics, including case-mix index (CMI). The AutoDx tool was developed utilizing tools existing within the electronic health record, and is based on the generation of messages when clinical conditions are met. These messages appear within provider notes and required little to no interaction. Initial diagnoses included in the tool were electrolyte deficiencies, obesity, and malnutrition. The tool was piloted in a cohort of Hospital Medicine providers, then expanded to the Neuro Intensive Care Unit (NICU), with addition diagnoses being added. The initial Hospital Medicine implementation evaluation included 590 encounters pre- and 531 post-implementation. The volume of coding queries decreased 57% (p < 0.0001) for the targeted diagnoses compared with 6% (p = 0.77) in other high-volume diagnoses. In the NICU cohort, 829 encounters pre-implementation were compared with 680 post. The proportion of AutoDx coding queries compared with all other coding queries decreased from 54.9 to 37.1% (p < 0.0001). During the same period, CMI demonstrated a significant increase post-implementation (4.00 vs. 4.55, p = 0.02). The real-time documentation assistance tool led to a significant decrease in coding queries for targeted diagnoses in two unique provider cohorts. This improvement was also associated with a significant increase in CMI during the implementation time period.