The rapid advancement of Low-Power Wide Area Networks (LPWANs), particularly Long Range (LoRa) systems, has positioned them as a cornerstone for Next-Generation Internet of Things (NG-IoT) applications within 5G/6G ecosystems. Despite their long-range and low-power advantages, achieving high energy efficiency in LoRa networks remains a significant challenge in highly dynamic environments. Traditional terrestrial gateway deployments often suffer from coverage gaps and non-line-of-sight propagation, while satellite-based alternatives incur excessive energy consumption and prohibitive latency. To address these limitations, we propose a multi-UAV architecture where unmanned aerial vehicles (UAVs) serve as mobile LoRa gateways to dynamically collect data from ground-based end devices (EDs). We formulate a joint optimization problem to maximize the system's weighted energy efficiency by jointly optimizing spreading factors, transmission powers, UAV trajectories, and ED-UAV associations. This problem is transformed into a partially observable stochastic game (POSG), which we solve using our proposed Green LoRa Multi-Agent Proximal Policy Optimization (GLo-MAPPO). Our framework leverages centralized training with decentralized execution (CTDE) and is enhanced by a gain-based ED-UAV association scheme. Simulation results show that GLo-MAPPO significantly outperforms state-of-the-art multi-agent reinforcement learning (MARL) benchmarks in energy efficiency and power consumption across varying network densities. Furthermore, ablation studies validate the necessity of each optimization component and the effectiveness of the proposed association scheme.

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