Guardian Waiting Shelters (GWSs) are an essential component of the Malawi’s health care system as they serve as a temporary home for patient guardians while taking care of their relatives admitted to the hospital, and expectant mothers. Although GWSs play a crucial role in Malawi’s healthcare system, past studies have primarily concentrated on maternity waiting homes, neglecting the role and importance of GWSs. The study examines GWS management structures and conditions, as well as guardian satisfaction and perception of health risks related to GWS use. In this explanatory sequential mixed methods design, we assessed 12 GWSs from southern region of Malawi. Qualitative data included interviews (n = 149) and focus group discussions with patient guardians (n = 72), interviews with GWS caretakers (n = 5), representatives from Hospital Management (n = 12) and Hospital Advisory Committees (n = 11). Lack of guidelines and standards for GWSs resulted in creating a customized facility checklist to quantitatively assess infrastructure present at GWSs (n = 12). Descriptive statistics and qualitative thematic analysis were utilized for data analysis, and a problem tree analysis was used to triangulate and summarize the findings. A total of 249 participants participated in the study. Each GWS had an average of 100 users daily, primarily adult females (71%). No one was accountable for GWS operation and maintenance due to the lack of a management hierarchy. GWS infrastructure conditions were poor, with inadequate functional sleeping rooms, insufficient access to water, sanitation and hygiene facilities. Notably, 50% of the GWSs lacked water access, and a quarter had non-functional toilets. Guardians felt unsafe and at risk of disease transmission when staying within GWS. Study findings highlight lack of clear, consistent GWS ownership as a root cause of challenges in GWSs. Clear policy and operational standards must be established for effective management and smooth functioning of GWSs.