We examined the effect of estimation methods, maximum likelihood (ML), unweighted least squares (ULS), and diagonally weighted least squares (DWLS), on three population SEM (structural equation modeling) fit indices: the root mean square error of approximation (RMSEA), the comparative fit index (CFI), and the standardized root mean square residual (SRMR). We considered different types and levels of misspecification in factor analysis models: misspecified dimensionality, omitting cross-loadings, and ignoring residual correlations. Estimation methods had substantial impacts on the RMSEA and CFI so that different cutoff values need to be employed for different estimators. In contrast, SRMR is robust to the method used to estimate the model parameters. The same criterion can be applied at the population level when using the SRMR to evaluate model fit, regardless of the choice of estimation method.