The number of people living with chronic conditions is increasing worldwide with most of these people receiving the needed healthcare services in primary healthcare (PHC) settings. The objective of this study was to explore the main challenges and barriers that PHC providers confront while treating multimorbid patients. This is a qualitative study utilising semi-structured individual in-depth interviews. The study took place in Vlora City, which is the biggest city located in south Albania. Τhe two biggest PHC centres of the city were enrolled. Purposive sampling method was used to recruit PHC practitioners. Main criteria of participation in the study were being fully employed at the enrolled primary care centres, having worked for at least 1 year and to deal with multimorbid patients in daily practice. Data collection took place from September 2019 to January 2020. In total, 36 semi-structured interviews took place with 23 (63.9%) nurses and 12 (33.3%) physicians (general practitioners/family doctors). Communication problems and disputes, lack of materials/equipment and the inappropriate infrastructure, miscommunication and problems in doctor-nurse relationships, coordination problems, lack of protocols and problems in the referral system were reported as the main challenges and barriers that the PHC personnel confront. The findings of this study are critical in understanding challenges that PHC personnel face when dealing with multimorbid patients in PHC settings. The emerged knowledge contributes significantly in a better understanding of the actual situation and to inform health policy makers on how to deal with the existing problems.