A novel, portable chemiluminescence (CL) sensing platform powered by deep learning and smartphone integration has been developed for cost-effective and selective glucose detection. This platform features low-cost, wax-printed micro-pads (WPµ-pads) on paper-based substrates used to construct a miniaturized CL sensor. A 3D-printed black box serves as a compact WPµ-pad sensing chamber, replacing traditional bulky equipment, such as charge coupled device (CCD) cameras and optical sensors. Smartphone integration enables a seamless and user-friendly diagnostic experience, making this platform highly suitable for point-of-care (PoC) applications. Deep learning models significantly enhance the platform’s performance, offering superior accuracy and efficiency in CL image analysis. A dataset of 600 experimental CL images was utilized, out of which 80% were used for model training, with 20% of the images reserved for testing. Comparative analysis was conducted using multiple deep learning models, including Random Forest, the Support Vector Machine (SVM), InceptionV3, VGG16, and ResNet-50, to identify the optimal architecture for accurate glucose detection. The CL sensor demonstrates a linear detection range of 10–1000 µM, with a low detection limit of 8.68 µM. Extensive evaluations confirmed its stability, repeatability, and reliability under real-world conditions. This deep learning-powered platform not only improves the accuracy of analyte detection, but also democratizes access to advanced diagnostics through cost-effective and portable technology. This work paves the way for next-generation biosensing, offering transformative potential in healthcare and other domains requiring rapid and reliable analyte detection.