This article addresses the problem of missing process data in data‐driven dynamic modeling approaches. The key motivation is to avoid using imputation methods or deletion of key process information when identifying the model, and utilizing the rest of the information appropriately at the model building stage. To this end, a novel approach is developed that adapts nonlinear iterative partial least squares (NIPALS) algorithms from both partial least squares (PLS) and principle component analysis (PCA) for use in subspace identification. Note that the existing subspace identification approaches often utilize singular value decomposition (SVD) as part of the identification algorithm which is generally not robust to missing data. In contrast, the NIPALS algorithms used in this work leverage the inherent correlation structure of the identification matrices to minimize the impact of missing data values while generating an accurate system model. Furthermore, in computing the system matrices, the calculated scores from the latent variable methods are utilized as the states of the system. The efficacy of the proposed approach is shown via simulation of a nonlinear batch process example.