The Internet of Things (IoT) is a novel networking paradigm which allows the communication among all sorts of physical objects over the Internet. The IoT defines a world-wide cyber-physical system with a plethora of applications in the fields of domotics, e-health, goods monitoring and logistics, among others. The use of cross-layer communication schemes to provide adaptive solutions for the IoT is motivated by the high heterogeneity in the hardware capabilities and the communication requirements among things. In this paper, a novel cross-layer module for the IoT is proposed to accurately capture both the high heterogeneity of the IoT and the impact of the Internet as part of the network architecture. The fundamental part of the module is a mathematical framework, which is developed to obtain the optimal routing paths and the communication parameters among things, by exploiting the interrelations among different layer functionalities in the IoT. Moreover, a cross-layer communication protocol is presented to implement this optimization framework in practical scenarios. The results show that the proposed solution can achieve a global communication optimum and outperforms existing layered solutions. The novel cross-layer module is a primary step towards providing efficient and reliable end-to-end communication in the IoT.