IEEE 802.11ax (Wi-Fi 6) technologies provide high capacity, low latency, and increased security. While many network researchers have examined Wi-Fi security issues, the security implications of 802.11ax have not been fully explored yet. Therefore, in this paper, we investigate how security protocols (WPA2, WPA3) affect TCP/UDP throughput in IEEE 802.11ax client–server networks using a testbed approach. Through an extensive performance study, we analyze the effect of security on transport layer protocol (TCP/UDP), internet protocol layer (IPV4/IPV6), and operating systems (MS Windows and Linux) on system performance. The impact of packet length on system performance is also investigated. The obtained results show that WPA3 offers greater security, and its impact on TCP/UDP throughput is insignificant, highlighting the robustness of WPA3 encryption in maintaining throughput even in secure environments. With WPA3, UDP offers higher throughput than TCP and IPv6 consistently outperforms IPv4 in terms of both TCP and UDP throughput. Linux outperforms Windows in all scenarios, especially with larger packet sizes and IPv6 traffic. These results suggest that WPA3 provides optimized throughput performance in both Linux and MS Windows in 802.11ax client–server environments. Our research provides some insights into the security issues in Gigabit Wi-Fi that can help network researchers and engineers to contribute further towards developing greater security for next-generation wireless networks.