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Abstract Additive manufacturing (AM) has revolutionized the way we design, prototype, and produce complex parts with unprecedented geometries. However, the lack of understanding of the functional properties of 3D-printed parts has hindered their adoption in critical applications where reliability and durability are paramount. This paper proposes a novel approach to the functional qualification of 3D-printed parts via physical and digital twins. Physical twins are parts that are printed under the same process conditions as the functional parts and undergo a wide range of (destructive) tests to determine their mechanical, thermal, and chemical properties. Digital twins are virtual replicas of the physical twins that are generated using finite element analysis (FEA) simulations based on the 3D shape of the part of interest. We propose a novel approach to transfer learning, specifically designed for the fusion of diverse, unstructured 3D shape data and process inputs from multiple sources. The proposed approach has demonstrated remarkable results in predicting the functional properties of 3D-printed lattice structures. From an engineering standpoint, this paper introduces a comprehensive and innovative methodology for the functional qualification of 3D-printed parts. By combining the strengths of physical and digital twins with transfer learning, our approach opens up possibilities for the widespread adoption of 3D printing in safety-critical applications. Methodologically, this work presents a significant advancement in transfer learning techniques, specifically addressing the challenges of multi-source (e.g., digital and physical twins) and multi-input (e.g., 3D shapes and process variables) transfer learning.