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To expand the use of cognitive diagnosis models (CDMs) to longitudinal assessments, this study proposes a three-step cognitive diagnosis learning model with covariates by integrating a general CDM and a latent transition model. The proposed model assesses students’ learning trajectories with respect to attribute mastery statuses and evaluates covariate effects on both the initial state and transition probabilities. Because stepwise approaches generally yield downward-biased estimates (Di Mari et al., 2016; Vermunt, 2010), a correction for classification error probabilities (CEPs) is considered.