Background: The public perceived negative attitudes and poor performance by some nurses, implying low moral competence levels. To determine how nurses handle moral issues in nursing practice, this study explored the challenges encountered and strategies employed by nurses when confronted with moral decisions. Methods: This study employed a qualitative research design utilizing in-depth interviews conducted by twenty nurse informants from hospitals in Iligan City, Philippines, recruited through a purposive sampling technique. A researcher-made interview guide with open-ended questions was utilized. The interviews were recorded, transcribed, and thematically analyzed. Results: The emergent themes are “predicaments toward patient and family issues” with two sub-themes (patient/family non-conforming decisions and dealing with emotionally burdened family members), “recognition of own weaknesses and shortcomings” with four sub-themes (infrequent performance of emotional care, insufficient provision of comfort, interference with the patient’s privacy, and delays in care due to prioritization), and “conflict with superiors”. Several strategies were employed to effectively address the moral challenges encountered. Conclusion: Moral competence is inherent in nurses, as they exhibit moral judgment and skills in overcoming the moral challenges encountered. However, there are moral issues beyond control in patient care. Therefore, hospital administrators may conduct a program to enhance the nurses’ competence to handle moral challenges and prevent moral distress, which will improve nursing practice.