The widespread adoption of additive manufacturing (AM) in critical industrial sectors, particularly aerospace, has highlighted concerns regarding intellectual property protection, supply chain integrity, and part authentication. This paper presents an advanced dual-fingerprint authentication framework for cold spray AM parts that combines inherent geometric features with engineered magnetic patterns, creating a robust defense against counterfeit parts while protecting valuable manufacturing intellectual property. Our authentication system leverages two complementary physical fingerprints. The first exploits the inherent stochastic nature of the cold spray process, where process variations and particle deposition dynamics generate unique, physically unclonable geometric patterns on each part's surface. These geometric fingerprints are captured through both high-resolution laser-based and low-resolution vision-based 3D scanning systems, providing flexibility in implementation while maintaining authentication reliability. We developed a Scale-Invariant Feature Transform (SIFT) based algorithm to compute similarity scores between geometric fingerprints, enabling robust part authentication across various scanning angles. The second authentication factor introduces a novel magnetic fingerprinting methodology. During the manufacturing process, we strategically embed nickel deposits within the aluminum substrate using a masked deposition technique in intermediate layers. The distinct magnetic properties between nickel and aluminum create a unique magnetic signature that can be detected non-destructively when the part is magnetized. We developed a precision magnetic mapping system that integrates a gaussmeter with a two-axis motion platform to accurately capture these magnetic patterns. To preserve the confidentiality of fingerprint information throughout the supply chain while enabling secure authentication, we implement a learning-with-error (LWE) encryption scheme. The magnetic fingerprint serves as an encryption key for the geometric fingerprint data, generating a secure label that accompanies the part. For authentication, users employ a specialized scanner that captures both the magnetic key and the current part's geometric fingerprint. The system decrypts the label using the magnetic key and compares the recovered geometric fingerprint with the newly scanned one, authenticating the part based on the similarity score. The significance of this work extends beyond basic part authentication. By combining natural and engineered physical features, our system creates a formidable barrier against reverse engineering and unauthorized replication, thereby protecting proprietary manufacturing processes and intellectual property. The non-destructive nature of both geometric and magnetic fingerprint acquisition ensures that authentication can be performed repeatedly throughout the part's lifecycle without compromising its structural integrity. This is particularly crucial for aerospace and other critical applications where cold spray AM parts are increasingly deployed. Furthermore, the system's ability to authenticate parts without exposing sensitive fingerprint data during transit enhances supply chain security, effectively preventing the infiltration of counterfeit parts that could compromise system performance and safety. Experimental validation demonstrates the system's effectiveness in authenticating cold spray AM parts while maintaining stringent security standards.