A measurement setup for differential sampling of AC waveforms based on a programmable Josephson voltage standard, with an integrating sampler, Keysight 3458, and a Δ-Σ analogue-to-digital converter, NI PXI-5922, is described. The system operates in several circuit configurations with different synchronization and triggering schemes. In particular, the focus is on how the filters implemented in the samplers affect sampling measurements. Numerical simulations on the frequency response characteristics of low-pass and finite impulse response filters for the samplers in differential sampling were performed, and the RMS amplitude of the fundamental for waveforms generated from an AC source in a voltage range of 1 V ≤ V ≤ 7.07 V and a frequency range of 40 Hz ≤ f ≤ 1.02 kHz was measured. The RMS amplitudes measured with the different samplers coincided within a few parts in 107 at frequencies below 100 Hz. However, the difference between the amplitudes increased with frequency, mainly due to the dramatic change of the value obtained with the integrating sampler. The difference reached up to −27 µV/V at 1.02 kHz. This feature is inferred to originate from the difference in the bandwidths for the two samplers. The stability of output waveforms for an AC source, APx-555, which could serve as a transfer standard in the framework of an on-site comparison of two independent differential sampling setups, is evaluated.