As digital ecosystems evolve into increasingly complex networks, harnessing their collective potential becomes paramount. This article focuses on developing software for smart ecosystems by programming their underlying System-of-Systems (SoS)—a domain ripe with opportunities and challenges. We propose the Holon Programming Model (HPM), which adds the programmability aspect to the holonic architecture of SoS and will pave the way for more integrated and adaptable systems. Demonstrating the HPM’s utility, we show how developers can program diverse behaviours and execute operations within the disaster management ecosystem, aiming to inspire and motivate software developers to explore the potential of SoS-level applications, which are fundamental for smart ecosystems.