Synchronous Flooding (SF) protocols can enhance the wireless connectivity between Internet of Things (IoT) devices. However, existing SF solutions fail to introduce sufficient security measures due to strict time synchronisation requirements, making them vulnerable to malicious actions. Our paper presents a design paradigm for encrypted SF communications. We describe a mechanism for synchronising encryption parameters in a network-wide fashion. Our solution operates with minimal overhead and without compromising communication reliability. Evaluating our paradigm on a real-world, large-scale IoT testbed, we have proven that a communication layer impervious to a range of attacks is established without sacrificing the network performance.