In this study, software-based countermeasures against a side-channel cryptanalysis of the Rabbit stream cipher were developed using Moteiv’s Tmote Sky, a popular wireless sensor mote based on the Berkeley TelosB, as the target platform. The countermeasures build upon previous work by improving mask generation, masking and hiding other components of the algorithm, and introducing a key refreshment scheme. Our contribution brings improvements to previous countermeasures making the implementation resistant to higher-order attacks. Four functional metrics, namely resiliency, robustness, resistance, and scalability, were used for the assessment. Finally, performance costs were measured using memory usage and execution time. In this work, it was demonstrated that although attacks can be feasibly carried out on unprotected systems, the proposed countermeasures can also be feasibly developed and deployed on resource-constrained devices, such as wireless sensors.