We consider the problem of occupancy estimation in buildings using available environmental information. In particular, we study the problem of how to collect data that is informative enough for occupancy estimation purposes. We thus propose an application-oriented input design approach for designing the ventilation signal to be used while collecting the system identification datasets. The main goal of the method is to guarantee a certain accuracy in the estimated occupancy levels while minimizing the experimental time and effort. To take into account potential limitations on the actuation signals we moreover formulate the problem as a recursive nonlinear and nonconvex optimization problem, solved then using exhaustive search methods. We finally corroborate the theoretical findings with some numerical examples, which results show that computing ventilation signals using experiment design concepts leads to occupancy estimator performing 4 times better in terms of Mean Square Error (MSE).