Low-power operating system runtimes used on IoT microcontrollers typically provide rudimentary APIs, basic connectivity and, sometimes, a (secure) firmware update mechanism. In contrast, on less constrained hardware, networked software has entered the age of serverless, microservices and agility. With a view to bridge this gap, in the paper we design Femto-Containers, a new middleware runtime which can be embedded on heterogeneous low-power IoT devices. Femto-Containers enable the secure deployment, execution and isolation of small virtual software functions on low-power IoT devices, over the network. We implement Femto-Containers, and provide integration in RIOT, a popular open source IoT operating system. We then evaluate the performance of our implementation, which was formally verified for fault-isolation, guaranteeing that RIOT is shielded from logic loaded and executed in a Femto-Container. Our experiments on various popular microcontroller architectures (Arm Cortex-M, ESP32 and RISC-V) show that Femto-Containers offer an attractive trade-off in terms of memory footprint overhead, energy consumption, and security.