Determining the number of factors in exploratory factor analysis is arguably the most crucial decision a researcher faces when conducting the analysis. While several simulation studies exist that compare various so-called factor retention criteria under different data conditions, little is known about the impact of missing data on this process. Hence, in this study, we evaluated the performance of different factor retention criteria--the Factor Forest, parallel analysis based on a principal component analysis as well as parallel analysis based on the common factor model and the comparison data approach--in combination with different missing data methods, namely an expectation-maximization algorithm called Amelia, predictive mean matching, and random forest imputation within the multiple imputations by chained equations (MICE) framework as well as pairwise deletion with regard to their accuracy in determining the number of factors when data are missing. Data were simulated for different sample sizes, numbers of factors, numbers of manifest variables (indicators), between-factor correlations, missing data mechanisms and proportions of missing values. In the majority of conditions and for all factor retention criteria except the comparison data approach, the missing data mechanism had little impact on the accuracy and pairwise deletion performed comparably well as the more sophisticated imputation methods. In some conditions, especially small-sample cases and when comparison data were used to determine the number of factors, random forest imputation was preferable to other missing data methods, though. Accordingly, depending on data characteristics and the selected factor retention criterion, choosing an appropriate missing data method is crucial to obtain a valid estimate of the number of factors to extract.