Malicious URLs provide adversarial opportunities across various industries, including transportation, healthcare, energy, and banking which could be detrimental to business operations. Consequently, the detection of these URLs is of crucial importance however, current Machine Learning (ML) models are susceptible to backdoor attacks. These attacks involve manipulating a small percentage of training data labels, such as Label Flipping (LF), which changes benign labels to malicious ones and vice versa. This manipulation results in misclassification and leads to incorrect model behavior. Therefore, integrating defense mechanisms into the architecture of ML models becomes an imperative consideration to fortify against potential attacks. The focus of this study is on backdoor attacks in the context of URL detection using ensemble trees. By illuminating the motivations behind such attacks, highlighting the roles of attackers, and emphasizing the critical importance of effective defense strategies, this paper contributes to the ongoing efforts to fortify ML models against adversarial threats within the ML domain in network security. We propose an innovative alarm system that detects the presence of poisoned labels and a defense mechanism designed to uncover the original class labels with the aim of mitigating backdoor attacks on ensemble tree classifiers. We conducted a case study using the Alexa and Phishing Site URL datasets and showed that LF attacks can be addressed using our proposed defense mechanism. Our experimental results prove that the LF attack achieved an Attack Success Rate (ASR) between 50-65% within 2-5%, and the innovative defense method successfully detected poisoned labels with an accuracy of up to 100%.