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To date, no information is available about the effect of structural and process factors of nutritional care on the prevalence of malnutrition over time in the long-term care sector. This study analyzes the trend of malnutrition prevalence rates between 2007 and 2011 in the long-term care sector, and the related effects of(1) process indicators such as nutritional screening and treatment and 2) structural indicators (guideline, protocol or nutritional screening policy). From 2007 to 2011, the Dutch National Prevalence Measurement of Care Problems (LPZ) was performed in Dutch long-term care organizations using a standardized questionnaire involving measurements at institutional, ward and resident level. The data were analyzed by mixed-linear regression for longitudinal data. Presence of malnutrition was assessed by BMI, undesired weight loss and nutritional intake. Seventy-four care homes were included (26,101 residents). The malnutrition prevalence trend significantly decreased (P < 0.001) from 26% to 18% from 2007 to 2011. In the final model of the mixed effects analysis only the interacted process indicators nutritional screening and oral nutritional supplementation (ONS) were significant in influencing malnutrition prevalence rates over time. Structural indicators had no impact on the malnutrition prevalence over time. In conclusion, over time a lower prevalence of malnutrition is associated with a higher degree of nutritional screening. As might be expected, a higher prevalence of malnutrition is associated with higher use of ONS. Structural nutritional screening is an important intervention to tackle the problem of malnutrition in the long term care sector.