Wireless surface electromyography (sEMG) sensors are very practical in that they can be worn freely, but the radio link between them and the receiver might cause unpredictable latencies that hinder the accurate synchronization of time between multiple sensors, which is an important aspect to study, e.g., the correlation between signals sampled at different sites. Moreover, to minimize power consumption, it can be useful to design a sensor with multiple clock domains so that each subsystem only runs at the minimum frequency for correct operation, thus saving energy. This paper presents the design, implementation, and test results of an sEMG sensor that uses Bluetooth Low Energy (BLE) communication and operates in three different clock domains to save power. In particular, this work focuses on the synchronization problem that arises from these design choices. It was solved through a detailed study of the timings experimentally observed over the BLE connection, and through the use of a dual-stage filtering mechanism to remove timestamp measurement noise. Time synchronization through three different clock domains (receiver, microcontroller, and ADC) was thus achieved, with a resulting total jitter of just 47 µs RMS for a 1.25 ms sampling period, while the dedicated ADC clock domain saved between 10% to 50% of power, depending on the selected data rate.