In large-scale studies, uncontrolled systematic variability introduced during sample preparation, processing, and storage can interfere with the detection of subtle biological signals. This study evaluates storage conditions, including two sample preparation methods and storage durations, to minimize systematic variability in the analysis of extracted lipids from latent fingerprints. In the traditional approach, samples are prepared immediately, stored as lipid extracts, and processed in multiple batches. In an alternative method, samples are stored directly on the deposition foil, and preparation is delayed until all can be processed in a single batch. Storage duration is evaluated to determine if shorter storage with analysis in multiple batches is more effective than longer storage with analysis in a single batch. Our findings demonstrate that storage of latent fingerprint samples on the deposition foil is a viable option, with minimal degradation of key features even after eight months of storage. While some differences in lipid profiles were observed across storage conditions, these differences were minor and would likely have little impact in larger studies where biological variability is greater. These insights offer practical guidance for implementing latent fingerprint sampling in large-scale studies by identifying optimal conditions that preserve sample quality and streamline workflows.