Background/Objectives: High levels of emotional intelligence (EI) and resilience in primary care physicians (PCPs) can help them communicate better with patients, build stronger relationships with colleagues, and foster a positive and collaborative workplace. However, studies have indicated that primary care physicians (PCPs) often do not focus enough on developing these skills. Consequently, the purpose of this mixed methods study was to evaluate the effectiveness of an experiential online training (EOT) intervention in enhancing the EI and resilience of PCPs who treat patients with chronic respiratory diseases (CRDs). Methods: A total of 46 PCPs from Greece participated in a 25-hour EOT program, which focused on counseling skills for lifestyle change and breathing techniques for self-regulation. Quantitative data were collected using the Trait Emotional Intelligence Questionnaire-Short Form (TEIQue-SF) and the Connor–Davidson Resilience Scale (CD-RISC-25) before, immediately after, and three months post-intervention. Additionally, qualitative data were obtained through written reflections from participants regarding their clinical practice. Results: The results revealed significant improvements in EI and resilience scores immediately after the intervention (ΕΙ: 5.13, SD: 0.65 vs. 5.3, SD: 0.57, p = 0.007; resilience: 76.6, SD: 11.75 vs. 79.83, SD: 10.24, p = 0.029), as well as at the three-month follow-up (ΕΙ: 5.3, SD: 0.57 vs. 5.36, SD: 0.48, p = 0.007; resilience: 79.83, SD: 10.24 vs. 81.03, SD: 7.86, p = 0.029). The thematic analysis of qualitative data identified improvements in five key themes: communication skills, stress management, emotional awareness, resilience, and patient care. Participants reported feeling more confident, empathetic, and effective when interacting with patients, particularly those from diverse backgrounds. The convergence of the quantitative and qualitative findings showed the efficacy of the EOT intervention in enhancing PCPs’ EI, resilience, well-being, and, ultimately, their practice.