This article presents findings on the consequences of matrix sampling of context questionnaires for the generation of plausible values in large-scale assessments. Three studies are conducted. Study 1 uses data from PISA 2012 to examine several different forms of missing data imputation within the chained equations framework: predictive mean matching, Bayesian linear regression, and proportional odds logistic regression. We find that predictive mean matching accurately reproduces the marginal distributions of the missing context questionnaire data due to matrix sampling. Study 2 uses data from PISA 2006 to examine the consequences of imputing context questionnaire data in terms of the generation of plausible values. We find that imputing context questionnaire data with predictive mean matching and using the imputed data to produce the plausible values yields very close approximation of the original marginal distributions but leads to underestimation of the correlation structure of the context questionnaire items. Study 3 examines imputation and plausible values generation within a partially balanced incomplete block design. We find that imputation within this design accurately reproduces the original marginal distributions and retains the correlation structure of the data. Implications for context questionnaire development are discussed.