The rapid evolution of manufacturing processes driven by Industry 4.0 demands systems capable of quickly adapting to dynamic market conditions and evolving customer needs. Agile manufacturing emphasizes flexibility, adaptability, and real-time responsiveness, posing challenges in run-time value chain analysis (VCA), including cost flows and production times. This paper presents a novel two-stage VCA approach using an activity-based costing mechanism via microservices to address these challenges. The VCA system enables real-time cost accounting and decision-making, supporting both pre- and post-production VCA, contrasting with traditional methods that rely on historical data. The first stage involves top-down cost calculations from resources to microservices. In contrast, the second focuses on constructing efficient manufacturing activities based on product requirements, allowing for granular analysis of costs and production times across microservices, activities, broader business processes, and finally, cost objects (e.g., customized products, batches of products, or customer invoices). The approach is validated through a proof-of-concept implementation of the VCA system integrated with the Eclipse Arrowhead framework and simulating Fischertechnik indexed line milling, drilling, and conveying operations. The results demonstrate the effectiveness of the proposed method in providing detailed insights into costs and production times, enhancing the efficiency and competitiveness of agile manufacturers.