This study investigates the role of integrated digital technologies and structured, multi-layered decision-making in enhancing warehouse operations and productivity. By comparing two warehouses with different levels of technological adoption—focusing on Shuttle-Based Storage and Retrieval Systems (SBS/RS), Supervisory Control and Data Acquisition (SCADA), Warehouse Management Systems (WMS), Track-Pod, and the Trevio Warehouse platform—the research examines impacts on workflows, labor productivity, and process stability. A key focus is how strategic, tactical, and operational decision-making layers interact to support effective technology adoption. Using a two-stage methodology—qualitative case study analysis and quantitative factorial evaluation—the study provides a comprehensive assessment of technology impacts. Results show that warehouses using integrated digital technologies with data-driven, multi-level decision-making achieve significantly greater labor productivity, operational stability, and scalability. These findings underscore the importance of aligning technological investments with decision frameworks to maintain long-term competitiveness in complex logistics environments.