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• Background In the cannabis industry, achieving accurate analytical test results is complex, hindered by challenges such as sampling issues, sample preparation, cross-contamination, and the choice of analytical methods. The heterogeneity of cannabis complicates obtaining representative samples, crucial for precise outcomes. Sample preparation is affected by the cannabis matrix's complexity, demanding specialized techniques for consistent analyte recovery. Cross-contamination during handling and the selection of analytical techniques like HPLC and GC also impact result accuracy. Furthermore, 'lab shopping' for favorable THC reports adds to the challenge, distorting product profiles and posing public health risks. • Objective This study investigates the impact of different milling instruments and conditions on cannabinoid recovery and sample throughput in analytical testing, and explores potential optimizations for cost, throughput, and contamination reduction, addressing gaps in current understanding. • Methods Samples of cannabis flower were milled according to various parameters and different mill types; an electric bladed mill and a food processor, with either reusable or single-use containers. • Results Investigations into milling methods for cannabis reveal that decarboxylation ratios or oxidation of THCA and CBDA flower do not significantly vary across different milling instruments or protocols. Single-use containers demonstrated improved cannabinoid recoveries, with specific conditions optimizing for THCA and THC or CBDA and CBD levels. • Conclusion This study delves into the impact of milling methods and operational parameters on cannabinoid analysis in cannabis, revealing that methodological choices significantly affect cannabinoid preservation. Notably, single-use containers at specific settings were optimal for maximizing THCA and THC levels, highlighting the importance of mill type and speed. However, the study also considers the operational and financial challenges of milling, suggesting that single-use containers may offer a balance between efficiency, sustainability, and cost-effectiveness. Furthermore, optimizing milling for THC preservation is economically advantageous, aligning operational efficiency with market demands. • Highlights The nuanced impact of milling conditions on cannabinoid preservation and extraction is highlighted.