Malnutrition results from inadequate nutrient intake, assimilation or utilisation, negatively impacting clinical outcomes and quality of life. It likely compromises gut barrier integrity, increasing intestinal permeability (IP), which impairs nutrient absorption or utilisation and increases the risk of infections and inflammation. This systematic review aims to examine the current evidence on the association between malnutrition and IP, identifying existing research gaps. A systematic search was conducted on PubMed, Scopus and Web of Science up to June 2024. According to PECOS strategy, ‘P’ = malnourished individuals or at risk of malnutrition, assessed for intestinal permeability; ‘E’ = malnutrition or risk of malnutrition; ‘C’ = well-nourished individuals; ‘O’ = increased intestinal permeability; and ‘S’ = all study types. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist was followed, and Study Quality Assessment Tools (NIH) were used for methodological quality analysis. Sixteen studies met the inclusion criteria, with a moderate/high risk of bias. Malnourished individuals exhibited increased IP across various conditions (e.g. anorexia nervosa, cancer and liver cirrhosis) or setting (hospital and community). A wide heterogeneity was observed in malnutrition assessment tools, which consider different parameters such as body mass index, body weight loss and food intake. Similarly, diverse biomarkers/methods for assessing IP, including direct and indirect approaches, were used. Despite methodological heterogeneity, findings show an association between malnutrition and increased IP. Standardised research, including comprehensive biomarker panels, is needed to improve comparability, facilitating the development of targeted interventions for preventing malnutrition and managing its complications.