Steel is not elemental iron but rather a group of iron-based alloys containing many elements, especially chromium, nickel, and molybdenum. Steel recycling is expected to promote efficient resource use. However, open-loop recycling of steel could result in quality loss of nickel and molybdenum and/or material loss of chromium. Knowledge about alloying element substance flow is needed to avoid such losses. Material flow analyses (MFAs) indicate the importance of steel recycling to recovery of alloying elements. Flows of nickel, chromium, and molybdenum are interconnected, but MFAs have paid little attention to the interconnected flow of materials/substances in supply chains. This study combined a waste input-output material flow model and physical unit input-output analysis to perform a simultaneous MFA for nickel, chromium, and molybdenum in the Japanese economy in 2000. Results indicated the importance of recovery of these elements in recycling policies for end-of-life (EoL) vehicles and constructions. Improvement in EoL sorting technologies and implementation of designs for recycling/disassembly at the manufacturing phase are needed. Possible solutions include development of sorting processes for steel scrap and introduction of easier methods for identifying the composition of secondary resources. Recovery of steel scrap with a high alloy content will reduce primary inputs of alloying elements and contribute to more efficient resource use.