Indoor environments affect occupant hygiene, comfort, and productivity. Special treatments, such as spraying essential oils, disinfectant gases, and water vapor or droplets, have been proposed to improve indoor comfort in recent years. Therefore, a method to control the concentrations of these beneficial substances is required. To control the indoor concentration distribution of various degradable substances emitted indoors, this article proposes a novel method that uses the linear relationship between the source and concentration distributions. The method was evaluated through numerical experiments using CFD. Furthermore, the effects of the deposition (Dep) and decomposition (Dec) of the substances on the performance were assessed. The method successfully determined the optimal emission intensities for each emission source to make the concentration field close to the objective—the uniform distribution—in the experiment. When substances decomposed in the air or were deposited on the walls, the performance of the optimal control decreased compared to the case without Dec or Dep. This indicated that the occurrence of Dec or Dep lowered the optimization performance by enhancing the unevenness of the concentration field in the area near the emission source and far from the source. The Dep case showed relatively lower performance than the Dec case because the Dep occurred more spatially unevenly than the Dec. In addition, the more emission sources employed, the smaller the gap between the objective and the optimized concentration field. This method will help control indoor air quality more efficiently.