Several designs of a Faraday Cup (FC) were assessed to understand their impact on the measurement of the ion current in the ion beam of two different low power electric thrusters, namely: a Field emission electric propulsion and a radiofrequency ion engine. These two thrusters are of interest because they are among the most popular in the space propulsion market. Moreover, on a more technical and scientific viewpoint, they allow the investigation of a wide range of conditions as they operate with different propellants (indium and xenon), different current densities and with ion energies from several hundreds to thousands of volts. Study outcomes show that for both thrusters the length of the FC is a key design parameter to passively mitigate overestimation of the measured ion current. Indeed, as opposed to other classical electric propulsion systems, such as Hall thrusters, measurements in the ion beam of FEEP and RF thrusters are strongly dependent on the ion-induced electron emission yield mostly due to the ion energy range (keV) at stake. The use of ion collectors made of non-standard materials with complex structure is also of great help to reduce the ion-induced electron yield. Indeed, for aluminium the yield decreases in average by 11±3% for the RIT and 60±8.4% for the FEEP depending on the collector structure dimensions. Finally, the true ion current can be properly retrieved with the right FC architecture where secondary electron emission effects are completely counter balanced.