Identifying those causes and parameters that affect the Quality of Service (QoS) of Voice-over-Internet Protocol (VoIP) through heterogeneous networks such as WiFi, WiMAX and between them are carried out using the OPNET simulation tool. Optimization of the network for both intra- and intersystem traffic to mitigate the deterioration of the QoS are discussed. The average value of the jitter of the VoIP traffic traversing through the WiFi-WiMAX network was observed to be higher than that of utilizing WiFi alone at some points in time. It is routinely surmised to be less than that of transiting across the WiFi network only and obviously higher than passing through the increased bandwidth network of WiMAX. Moreover, both the values of the packet end-to-end delay and the Mean Opinion Score (MOS) were considerably higher than expected. The consequences of this optimization, leading to a solution, which can ameliorate the QoS over these networks are analyzed and offered as the conclusion of this ongoing research.