Abstract Introduction Despite the high prevalence of malnutrition in patients at all levels of healthcare, early prevention and treatment of malnourished patients are often neglected and overlooked in clinical practice. The aim of this systematic literature review was to identify the factors considered most important by healthcare professionals in the identification and treatment of malnourished patients or those at risk of malnutrition. Methods A systematic literature review of qualitative research was conducted. Documents published in scientific journals in English from 2011 to 2021 were searched in the PubMed (MEDLINE), CINAHL and ProQuest databases. The results were analysed with a thematic analysis of qualitative research findings. Results From the search set of 1010 results, 7 sources were included in the final analysis. Factors identified by health professionals as important in the identification and treatment of malnourished patients in clinical practice were grouped into five themes: unclear organizational structure; indefinite structure of nutritional care; poor continuity of nutritional care; lack of knowledge and skills of health professionals; lack of time and human resources. Conclusions Health policy must provide resources for nutritional care for patients at all levels of health care on the initiative of the highest professional bodies at the state level. To improve the nutritional care of patients in clinical practice, the management of health care institutions must promote and enable the professional and organizational establishment of clinical nutrition as a regular medical activity of the institution, develop clinical nutritional pathways, and promote evidence-based clinical practice and interprofessional collaboration.