New Ways of Working (NWW) offices have detrimental effects on users’ satisfaction and productivity when planned without clear understanding of users’ space usage pattern. To deal with this problem, space usage analysis based on objective information is required. Of the various methods to estimate users’ space usage information, Bluetooth Low Energy (BLE) beacon has potentials and its estimation accuracy in offices was proved by several studies. However, the previous studies have limitations in that they did not test the estimation accuracy reflecting user’s non-sedentary state and a spatial characteristic of NWW offices, which is composed of various layouts of spaces. Thus, this study aims to prove the feasibilities of using BLE beacons in NWW offices by testing the estimation accuracy with a non-sedentary user in different spatial layouts (i.e., small office room and open space). To analyze the estimation accuracy, we defined the Coordinate Error (CE) which is the distance between the BLE beacon-estimated location and the actual user location. The average CE of total experiments in the small office room was 0.99 m and that of the open space was 3.40 m. The result indicates BLE beacon deployment strategies depending on spatial layouts are required for achieving a high estimation accuracy.