<p>An increasing number of laboratories are engaged in the preparation of DNA libraries for high-throughput sequencing (HTS). However, many HTS library preparation steps require costly reagents and equipment, including single-use consumables like tubes, which can be prohibitively expensive. Beyond economic concerns, the environmental impact of single-use consumables is a critical issue, as their extensive use contributes to laboratory-produced ecological waste. This study assesses the efficiency of a four-step cleaning protocol for microTUBE-50 AFA Fiber Screw-Caps commonly used in DNA shearing, a critical step in HTS library preparation. After each step of our protocol, we tested the amount of DNA residue remaining in tubes using the Quant-iT dsDNA High Sensitivity assay. Results suggest the protocol reduces DNA residues to levels below those that could impact subsequent library preparations. Consequently, this eco-friendly and cost-efficient cleaning protocol allows the reuse of already-used tubes, while maintaining fragmentation quality and tube integrity. This approach is a sustainable alternative for laboratories seeking to minimize single-use consumables, reduce waste, and lower the costs associated with genomics research.</p>