Providing long-term care for people living with chronic conditions is a key component of universal health coverage (UHC). To achieve UHC and address social determinants of health, the Malawian government launched the second health sector strategic plan (HSSPII) in 2017. Achieving its targets would require an understanding of contextual factors and mechanisms influencing HSSPII implementation. We explore health stakeholders’ experiences of planning and delivering chronic care services for rural trans-border communities in Malawi. We conducted 15 semi-structured interviews with health stakeholders in Phalombe district, Malawi near the Mozambique border. Respondents were selected through snowballing and purposively to ensure diversity of responses. We applied a thematic approach to data analysis. Respondents reported mixed experiences with implementing the strategy on ‘paper’, with operational difficulties reflecting on-the-ground realities. A key concern for respondents from public facilities was high influx of migrant patients from border communities in Mozambique, due to user-fees charged in their healthcare system. This resulted to acute shortage of medical supplies and continuous pressure on health personnel in healthcare provision, which hindered the effective implementation of UHC. Respondents reported high patient-workload compromised quality of care provided and served as demotivating factors, which posed as major obstacles to UHC attainment. Health providers also experienced difficulties screening and assessing patient eligibility for free healthcare, given the integration of bordering communities. This was attributed to a lack of national identification system, which has severe financial and logistical implications for UHC implementation. While the HSSPII and UHC goals aim to increase coverage and make healthcare services geographical accessible, patient access was crippled by transportation and medication costs in paying health facilities. Health policy makers and planners need to utilise a sector-wide approach that takes into account the operational realities on the ground in implementing UHC, to design innovative interventions that target these findings.