This study aims to investigate the effect of the Project-based Learning (PjBL) learning model and class differences based on online learning settings (synchronous, asynchronous, and mixed) on the analytical abilities of the Discovery Learning (DL), Interactive Demonstration (ID), and Inquiry Lessons (IL) models after adjusting for IQ of pre-service elementary teachers (PETs). The sample was randomly selected as 36 PETs who took science teaching courses in elementary schools. Data collection techniques using tests with indicators of analytical ability at the level of inquiry model stage include DL, ID, and IL. Data analysis was carried out quantitatively using two-way multivariate analysis of covariance with one covariate. The results showed that the PjBL model and the online learning setting each affected students' analytical skills in DL, ID, and IL, but after the learning model interacted with differences in online learning settings the results did not affect the analytical test results on the DL, ID, and IL models. This finding indicates that in an online learning design, the selection of project-based learning models can be effective if the right online learning setting is used, namely a combination of synchronous and asynchronous.