Depression and anxiety are common among people with HIV and are associated with inadequate viral suppression, disease progression, and increased mortality. However, depression and anxiety are underdiagnosed and undertreated in people with HIV owing to inadequate visit time and personnel availability. Conducting population-level depression and anxiety screening via the patient portal is a promising intervention that has not been studied in HIV care settings. We aimed to explore facilitators of and barriers to implementing population-level portal-based depression and anxiety screening for people with HIV. We conducted semistructured hour-long qualitative interviews based on the Consolidated Framework for Implementation Research with clinicians at an HIV clinic. A total of 10 clinicians participated in interviews. In total, 10 facilitators and 7 barriers were identified across 5 Consolidated Framework for Implementation Research domains. Facilitators included advantages of systematic screening outside clinic visits; the expectation that assessment frequency could be tailored to patient needs; evidence from the literature and previous experience in other settings; respect for patient privacy; empowering patients and facilitating communication about mental health; compatibility with clinic culture, workflows, and systems; staff beliefs about the importance of mental health screening and benefits for HIV care; engaging all clinic staff and leveraging their strengths; and clear planning and communication with staff. Barriers included difficulty in ensuring prompt response to suicidal ideation; patient access, experience, and comfort using the portal; limited availability of mental health services; variations in how providers use the electronic health record and communicate with patients; limited capacity to address mental health concerns during HIV visits; staff knowledge and self-efficacy regarding the management of mental health conditions; and the impersonal approach to a sensitive topic. We proposed 13 strategies for implementing population-level portal-based screening for people with HIV. Before implementation, clinics can conduct local assessments of clinicians and clinic staff; engage clinicians and clinic staff with various roles and expertise to support the implementation; highlight advantages, relevance, and evidence for population-level portal-based mental health screening; make screening frequency adaptable based on patient history and symptoms; use user-centered design methods to refine results that are displayed and communicated in the electronic health record; make screening tools available for patients to use on demand in the portal; and create protocols for positive depression and anxiety screeners, including those indicating imminent risk. During implementation, clinics should communicate with clinicians and clinic staff and provide training on protocols; provide technical support and demonstrations for patients on how to use the portal; use multiple screening methods for broad reach; use patient-centered communication in portal messages; provide clinical decision support tools, training, and mentorship to help clinicians manage mental health concerns; and implement integrated behavioral health and increase mental health referral partnerships.