Medical practitioners commonly deal with moral tensions and difficult choices in patient care, prompting increased attention to the concept of conscientious objection (CO). Spain’s health system currently offers no formal guidance on what constitutes valid reasons for CO, how it should be properly exercised, or how best to assist professionals who choose to invoke it. A well-defined procedural framework is therefore necessary. This framework must ensure responsible use of CO by clinicians while upholding its moral legitimacy and legal compliance, balancing respect for personal ethical convictions with patients’ entitlement to timely healthcare. The suggested approach specifies eligibility criteria for CO (individual reference, specific clinical context, ethical justification, assurance of non-discrimination, professional consistency, attitude of mutual respect, assurance of patient rights and safety) along with a step-by-step procedural pathway (notification and preparation, documentation and confidentiality, evaluation of prerequisites, non-abandonment, transparency, allowance for unforeseen objection, compensatory responsibilities, access to guidance and/or consultative advice, and organizational guarantee of professional substitution). The practical usefulness of this model is shown by applying it to a realistic clinical case scenario.