The current initiatives at European level urge more emphasis on the implementation of inquiry-based science education (IBSE). Although there are existing studies on the effect of IBSE on understanding science, fewer attempts have been made regarding the development of various inquiry skills. In this research, a model of consistent implementation of inquiry activities across the three subjects of mathematics, physics and informatics was developed and its efficacy with regard to selected inquiry skills development was examined. In order to evaluate the efficacy, a test assessing the level of inquiry skills development was designed. This test was taken by 300 high school students both before and after experimental teaching. In between students were exposed to coherent and intentional multidisciplinary inquiry-based learning within a period of approx. four months. The results showed a statistically significant increase on test scores that is gender independent, however the class specialization played a significant role. The results indicate that the designed model of coactive IBSE implementation is efficacious for inquiry skills development and therefore applicable in school practice.