Introduction: The present scientific article addresses about the problematic that the chain of custody has on the valuation of evidence and effective judicial protection in the criminal adversarial procedure, by means of a qualitative and varied methodology, where both the historical precedents of the subject and its current application are analyzed, based on a variety of methodologies such as: historical, logical, deductive, inductive, analytical, synthetic and dogmatic. Through the bibliographic review, the urgent need for a legislative intervention that safeguards the authenticity of the chain of custody and the valuation of evidence and effective judicial protection in the adversarial criminal procedure is evidenced. Objective: Therefore, the objective is to discover how the mismanagement of the chain of custody by the national police negatively affects the majority of criminal cases in the evaluation of the evidence by the Prosecutor's Office and even the jurisdictional body, which undermines the effective judicial protection that carries out the criminal prosecution, delegitimizing the integral judicial system in the application of the accusatory system. Methodology: For the proper elaboration, a qualitative approach was chosen and the use of several methods such as: historical/logical, in order to analyze the background and development of the topic; deductive/inductive, to move from general to specific concepts; analytical/synthetic, to deal with the implications and current legal issues; and finally, the dogmatic method, which is arbitrary and arises from the regulations and, ultimately, provides theoretical support for this topic. The technique was the bibliographic review. Results: It was determined that the current regulation in Ecuador on the chain of custody, valuation of evidence and effective judicial protection in the adversarial criminal procedure is insufficient, which leads to protection of the chain of custody while ensuring legal certainty and without violating rights. Conclusion: In this context, it is demanding that the national assembly, in this case the Ecuadorian legislators, intervene to guarantee an adequate regulation of the chain of custody; evaluation of evidence and effective judicial protection in the adversarial criminal procedure, ensuring legal certainty and without violating rights.