Indoor Positioning Systems (IPSs) are designed to provide solutions for location-based services. Wireless local area network (WLAN)-based positioning systems are the most widespread around the globe and are commonly found to have a ready-to-use infrastructure composed mostly of access points (APs). They provide useful information on signal strength to be processed by adequate location algorithms, which are not always capable of achieving the desired localization error only by themselves. In this sense, this paper proposes a new method to improve the accuracy of IPSs by optimizing some of their most relevant infrastructure components. Included are the arrangement of APs over the environment, the number of reference points (RPs), and the number of samples per location estimation test. A simulation environment is also proposed, in which the impact of key influencing factors on system accuracy is analyzed. Finally, a case study is simulated to validate an optimal combination of design parameters and its compliance with the requirements of localization error and the limited number of access points. Our simulation results clearly show that the desired localization accuracy, which is set as a goal, can be achieved while maintaining the factors already mentioned at minimal levels, which decreases both system deployment costs and computational effort.