The Australian Commission on Safety and Quality in Health Care (ACSQHC) coordinates nation‐wide audits of the National Inpatient Medication Chart (NIMC). Electronic Medication Management Systems (eMMS) are beginning to replace NIMCs in Australian hospitals. This article describes the NIMC audit experience in two Australian tertiary hospitals that have established eMMS. Medication charts at both hospitals were audited using the ACSQHC‐provided audit tools (2012 Version). At both hospitals, eMMS charts exhibited higher levels of compliance with audit criteria than NIMCs, except for documentation of indication for medication. With eMMS, both hospitals exceeded national averages on many audited parameters, with the exceptions of documentation of weight and indication for medication. eMMS produces clearer, more complete medication orders and patient information, which may improve quality and safety of prescribing and reduce medication errors. Feedback was provided to the ACSQHC regarding aspects of the NIMC audit that did not align with eMMS for consideration in future audits.