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Indoor positioning systems (IPS) are used to locate people or objects in environments where the global positioning system (GPS) fails. The commitment to make bluetooth low energy (BLE) technology the leader in IPS and their applications is clear: Since 2009, the Bluetooth Special Interest Group (SIG) has released several improved versions. BLE offers many advantages for IPS, e.g., their emitters or beacons are easily deployable, have low power consumption, give a high positioning accuracy and can provide advanced services to users. Fingerprinting is a popular indoor positioning algorithm that is based on the received signal strength (RSS); however, its main drawbacks are that data collection is a time-consuming and labor-intensive process and its main challenge is that positioning accuracy is affected by various factors. The purpose of this work was to develop a semi-automatic data collection support system in a BLE fingerprinting-based IPS to: (1) Streamline and shorten the data collection process, (2) carry out impact studies by protocol and channel on the static positioning accuracy related to configuration parameters of the beacons, such as transmission power (Tx) and the advertising interval (A), and their number and geometric distribution. With two types of systems-on-chip (SoCs) integrated in Bluetooth 5 beacons and in two different environments, our results showed that on average in the three BLE advertising channels, the configuration of the highest Tx (+4 dBm) in the beacons produced the best accuracy results. However, the lowest Tx (−20 dBm) did not worsen them excessively (only 11.8%). In addition, in both scenarios, when lowering the density of beacons by around 42.7%−50%, the error increase was only around 8%−9.2%.