Background In Malawi, community wide flooding, especially in high HIV burdened districts, continues to affect continuity of care and access to facilities. We explored the lived experiences of clients and healthcare workers (HCWs) to gain understanding of challenges and to propose interventions for improved ART care delivery. Methods Participants came six health facilities and surrounding communities impacted by flooding between Dec 2021-Apr 2022 in Chikwawa, Nsanje and Mulanje districts in Malawi. Facilities are supported by Partners in Hope, a local NGO and PEPFAR/USAID partner. We conducted In-depth interviews with (IDIs) ART clients identified through medical chart reviews and focus group discussions (FGDs) with HCWs. IDIs and FGDs were coded using inductive and deductive methods in Atlas.ti. Results We conducted IDIs with 23 respondents, of which, ten were women, ten experienced treatment interruption (>28 days without medication) and 17 relocated from their homes. The Six FGDs involved 37 HCWs. (21 ART providers; 16 lay cadre). In IDIs, most clients who relocated and lost livestock, possessions and ART medications. They travelling for income generation. Barriers to care included dangerous travel conditions, competing needs for time and fear of ill treatment at facilities. Some outreach clinics did not provide ART. Respondents were motivated to remain on care and motivators included fear of developing illnesses and HIV-status acceptance. All providers said that lack of standardized guidelines affected preparedness and response and they advocated for guidelines, stakeholder coordination and adequate resources. Most also reported personal physical exhaustion, damage to their own houses and property, and drug stock-outs. Documentation due to loss of registers was also mostly mentioned. Discussion Clients motivated to remain in care but face barriers and challenges. National flooding protocols, adequate resource planning and seasonal 6-month ART dispensing may improve ART outcomes.