Silver nanoparticles (AgNPs) are known for their unique plasmonic colors and interaction with light, making them ideal for color printing and data encoding. Traditional methods like electron beam lithography (EBL) and focused ion beam (FIB) milling, however, suffer from low throughput and high costs. In this paper, a scalable and cost‐efficient method is introduced for producing multiplexed plasmonic colors by in situ photoreducing AgNPs within microgel architectures with controlled porosity. Utilizing a digital micro‐mirror device (DMD)‐based flow microlithography system combined with a programmable dithering‐mask technique, the high‐throughput synthesis of shape or barcoded microparticles is facilitated, along with large‐scale, high‐resolution images embedded with hidden multiplexed plasmonic colors. This approach allows for a hidden multiplexed plasmonic color code library, significant enhancing the encoding capacity of barcode microparticles from 33 to 303 (a 1000‐fold increase). Additionally, quantitative agreement is achieved between chemically encrypted and optically decrypted plasmonic colors using a deep learning classifier. Moreover, the method also supports the production of large scale (>5.6 × 5.6 cm2), high‐resolution (>300 dpi) microgel arrays encrypted with multiple plasmonic colors in under 30 min. The multiplexed plasmonic coloration strategy in microgel architectures paves a new way for hidden data storage, secure optical labeling, and anti‐counterfeiting technologies.