This study aimed to investigate the effect of simulation and animation-integrated instructions (SAII) on pre-service science teacher trainees' conceptual understanding, motivation, and retention capability on acid-base chemistry and stoichiometry Learning. Quantitative-led partial mixed-method research was conducted. The quantitative part of the study used a pre-post-delayed quasi experimental design, while the qualitative part employed a thematic analysis design. Two intact classes with similar characteristics were used for the comprehensive sampling technique. The classes were randomly assigned to a treatment group (TG) and a comparison group (CG). Data on conceptual understanding and retention were collected using Acid-Base Chemistry and Stoichiometry Conceptual Understanding two-tier multiple-choice Test (ABSCUT). Data on motivation was collected using the mixed Chemistry Motivation Questionnaire (CMQ). The quantitative data were analyzed by independent sample t-test and ANCOVA, while the qualitative data was analyzed using a thematic analysis approach. The independent sample t-test was used to analyze conceptual understanding and motivation while ANCOVA was used to analyze delayed test after the intervention. The gain mean analysis result showed that a statistically significant difference between the two groups in conceptual understanding, in favor of the TG. Analysis for motivation indicated statistical significant difference between, in favor of the TG. The qualitative analysis also implied that most of the trainees in the TG showed higher motivation than the CG toward learning chemistry. The effects of SAII between male and female trainees in the TG showed no statistically significant difference in conceptual understanding, however, a statistically significant difference observed in terms of motivation in the TG. The ANCOVA results in the delayed-test analysis showed that the TG had higher retention than the CG. Based on the results, this study recommends that chemistry curriculum experts, chemistry curricular materials developers, and practitioners consider applying SAII for the teaching-learning process of chemistry in general and acid-base chemistry and stoichiometry in particular to enhance trainees‘ conceptual understanding, retention, and motivation to learn