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Bluetooth (BT) has revolutionized close-range communication enabling smart capabilities in everyday devices through wireless technology. One of the most important sub-domains of Internet-of-Things (IoT) specializes in the usage of BT technologies to develop smart homes and environments, which include hospitals, buildings, shopping facilities, etc. to offer a wide-range of features, like instantaneous and remote access to ventilation, lighting, security, localization, and tracking. However, the deployment of such features in smart infrastructures are typically unaccompanied by appropriate security measures that safeguard the data and protect its users. Towards this, we propose the ATLAS framework, which is composed of our novel IoT architecture and secure networking stack that can be used to anonymously localize and track smartphones and wearables by deploying multiple Bluetooth Low Energy (BLE) beacons across the environment. The proposed networking stack enables varying levels of encryption across all layers of the communication stack to ensure an easy-to-adopt, secure-by-design network architecture. We also deploy a novel data transformation and fingerprinting-based localization algorithm, which is highly effective in localizing user devices within a given area. The ATLAS framework is open-sourced at https://atlas-tuw.sourceforge.io to enable wide-spread adoption and further research and development.