Using Internet of Things (IoT) applications has been a growing trend in the last few years. They have been deployed in several areas of life including secure and sensitive sectors like military and health. In these sectors, sensory data is the main factor in any decision-making process. This introduces the need to ensure the integrity of data. Secure techniques are needed to detect any data injection attempt before catastrophic effects happen. Sensors have limited computational and power resources. This limitation creates a challenge to design a security mechanism that is both secure and energy-efficient. This work presents a Randomized Watermarking Filtering Scheme (RWFS) for IoT applications that provides en-route filtering to get rid of any injected data at an early stage of the communication. Filtering injected data is based on a watermark that is generated from the original data and embedded directly in random places throughout the packet's payload. The scheme uses homomorphic encryption techniques to conceal the report's measurement from any adversary. The advantage of homomorphic encryption is that it allows the data to be aggregated and, thus, decreases the packet's size. The results of our proposed scheme proved that it improves the security and energy consumption of the system as it mitigates some of the limitations in the existing works.