In this paper, we aimed to identify the dynamics of a crude distillation unit (CDU) using closed-loop data with NARX−NN and the Koopman operator in both linear (KL) and bilinear (KB) forms. A comparative analysis was conducted to assess the performance of each method under different experimental conditions, such as the gain, a delay and time constant mismatch, tight constraints, nonlinearities, and poor tuning. Although NARX−NN showed good training performance with the lowest Mean Squared Error (MSE), the KB demonstrated better generalization and robustness, outperforming the other methods. The KL observed a significant decline in performance in the presence of nonlinearities in inputs, yet it remained competitive with the KB under other circumstances. The use of the bilinear form proved to be crucial, as it offered a more accurate representation of CDU dynamics, resulting in enhanced performance.