The growing burden of expired medicines contributes to environmental contamination and landfill waste accumulation. Medicinal honey, with its non-toxic nature and potentially long shelf-life, represents a promising and underutilised therapeutic that avoids some of these issues. However, limited knowledge on how its antimicrobial properties change over time combined with a lack of reliable processes in the honey industry for measuring antimicrobial potential, hinder its clinical adoption. Using a diverse selection of 30 Australian honey samples collected between 2005 and 2007, we comprehensively evaluated their antibacterial and antifungal activity and pertinent physical and chemical properties with the aims of assessing the effect of long-term storage on activity, pinpointing factors associated with antimicrobial efficacy, and establishing robust assessment methods. Minimum inhibitory concentration (MIC) assays proved superior to the standard phenol equivalence assay in capturing the full range of antimicrobial activity present in honey. Correlations between activity and a range of physical and chemical properties uncovered significant associations, with hydrogen peroxide, antioxidant content, and water activity emerging as key indicators in non-Leptospermum honey. However, the complex nature and the diverse composition of honey samples precludes the use of high-throughput chemical tests for accurately assessing this activity, and direct assessment using live microorganisms remains the most economical and reliable method. We provide recommendations for different methods of assaying various honey properties, taking into account their accuracy along with technical difficulty and safety considerations. All Leptospermum and fourteen of seventeen non-Leptospermum honey samples retained at least some antimicrobial properties after 15-17 years of storage, suggesting that honey can remain active for extended periods. Overall, the results of this study will help industry meet the growing demand for high-quality, medicinally active honey while ensuring accurate assessment of its antimicrobial potential.