The deployment of LTE in unlicensed spectrum is a plausible solution to meet explosive traffic demand from mobile users. However, fair coexistence with the existing unlicensed technologies, mainly Wi-Fi, needs to be ensured before any such deployment. Duty cycled LTE (LTE-U) is a simple and an easily adaptable scheme which helps in fair coexistence with the Wi-Fi. Nonetheless, the immense deployment of Wi-Fi necessitates a user-oriented study to find the effects of LTE-U operation, primarily in scenarios where the LTE-U eNB remains hidden from Wi-Fi Access Point. To delineate these effects, we perform a user-level Transmission Control Protocol (TCP) and User Datagram Protocol (UDP) throughputs study of Wi-Fi in the presence of LTE-U using a testbed. Since, TCP is a more complicated protocol, we analyzed the Congestion Window and Round Trip Time data to comprehend the throughput results. This further explains the unfairness in throughput distribution among Wi-Fi users. Furthermore, we also notice inability among the disadvantaged users to receive the periodic Wi-Fi beacon frames successfully. The reasons and the subsequent consequences of throughput unfairness and beacon losses, are carefully elaborated. Also, to validate the beacon loss results, we present a beacon loss analysis which provides a mathematical expression to find the beacon loss percentage. Finally, we examine the results and highlight a need for incorporating additional functionalities in either LTE-U or Wi-Fi to overcome the present challenges. © Springer Nature Switzerland AG 2019.