The inclusion of covariates improves the prediction of class memberships in latent class analysis (LCA). Several methods for examining covariate effects have been developed over the past decade; however, researchers have limited to the comparisons of the performance among these methods in cases of the single-level LCA. The present study investigated the performance of three different methods for examining covariate effects in a multilevel setting. We conducted a simulation to compare the performance of the three methods when level-1 and level-2 covariates were simultaneously incorporated into the nonparametric multilevel latent class model to predict latent class membership at each level. The simulation results revealed that the bias-adjusted three-step maximum likelihood method performed equally well as the one-step method when the sample sizes were sufficiently large and the latent classes were distinct from each other. However, the unadjusted three-step method significantly underestimated the level-1 covariate effect in most conditions.