Numerous neuroscience studies demonstrate that when motor and cognitive tasks are performed simultaneously, there is dual-task interference. Experiments show that the cost is a temporal deterioration in motor functioning. However, there is no comprehensive research on the developmental costs of dual-task exercises incorporated into physical education (PE). Such an approach is called the interdisciplinary model of PE and is used to stimulate cognitive development. Therefore, there is a knowledge gap regarding the motor costs of methods based on this model, e.g., Eduball. The Eduball method integrates core academic subjects with PE using a set of educational balls printed with letters, numbers, and other signs. To fill this knowledge gap, we replicated the Eduball experiment, focusing on motor development. The half-year intervention occurred in one primary school class. The control group was a peer class participating in traditional PE, not based on dual tasks. We tested students’ space-time orientation and graphomotor, locomotor, and object control skills. We found no motor costs of the intervention. Eduball-based PE stimulated motor development as much as traditional PE. Our study suggests that methods based on the interdisciplinary model of PE are safe for motor development. As such, it is worth considering their use in children’s education.