Internet of Things (IoT) systems are becoming core building blocks for different services and applications supporting every day’s life. The heterogeneous nature of IoT devices and the complex use scenarios make it hard to build secure and private IoT systems. Physical-Layer Security (PLS) can lead to efficient solutions reducing the impact of the increasing security threats. In this work, we propose a new PLS-based IoT transmission scheme that offers a highly secured transmission probability, low-computational complexity, and reduced power consumption. We utilize 3-D stochastic geometry to model a more realistic IoT system and test our proposed scheme in different practical scenarios, where sensors, Access Points (APs), and eavesdroppers are randomly located in 3-D space. We focus on the system performance, in terms of Secrecy Outage Probability (SOP), and secured successful transmission probability (SSTP), using tight closed-form expressions. An optimization problem is developed to deduce the optimal sensors’ transmit power, the APs’ density, and the maximum number of transmission tentative, when maximizing the SSTP. The proposed scheme outperforms the baseline re-transmission scheme, in terms of SOP and SSTP based on analytical and simulation results. IEEE Scopus