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In the near future, the fifth-generation wireless technology is expected to be rolled out, offering low latency, high bandwidth and multiple antennas deployed in a single access point. This ecosystem will help further enhance various location-based scenarios such as assets tracking in smart factories, precise smart management of hydroponic indoor vertical farms and indoor way-finding in smart hospitals. Such a system will also integrate existing technologies like the Internet of Things (IoT), WiFi and other network infrastructures. In this respect, 5G precise indoor localization using heterogeneous IoT technologies (Zigbee, Raspberry Pi, Arduino, BLE, etc.) is a challenging research area. In this work, an experimental 5G testbed has been designed integrating C-RAN and IoT networks. This testbed is used to improve both vertical and horizontal localization (3D Localization) in a 5G IoT environment. To achieve this, we propose the DEep Learning-based co-operaTive Architecture (DELTA) machine learning model implemented on a 3D multi-layered fingerprint radiomap. The DELTA begins by estimating the 2D location. Then, the output is recursively used to predict the 3D location of a mobile station. This approach is going to benefit use cases such as 3D indoor navigation in multi-floor smart factories or in large complex buildings. Finally, we have observed that the proposed model has outperformed traditional algorithms such as Support Vector Machine (SVM) and K-Nearest Neighbor (KNN).