The development of a functional unmanned aerial vehicle (UAV) mounted aeromagnetic system requires integrating a magnetometer payload onboard a UAV platform in a manner that preserves the integrity of the total magnetic field measurements. One challenge when developing these systems is accounting for the sources of in-flight magnetic and electromagnetic interference signals that are greater than the resolvability threshold of the magnetometer. Electromagnetic interference generated by the platform has the potential to be mitigated using several techniques such as magnetic shielding, filtering, or compensation and can be attenuated by strategically positioning the magnetometer at a distance from the UAV. The integration procedure and selection of a mitigation strategy can be informed by characterizing the electromagnetic interference generated by the platform. Scalogram analysis is used to characterize the high-frequency electromagnetic signals generated by multirotor UAV electromagnetic motors. A low-sensitivity (7 nT) vector, fluxgate magnetometer is used to measure the electromagnetic interference generated by two unique multirotor UAVs in a controlled laboratory setting. Results demonstrate three spectrally distinct electromagnetic signals, each with unique frequency and amplitude, generated by each UAV platform. The frequency of these electromagnetic interference signals is found to be directly proportional to the applied rotation frequency of the electromagnetic motor. The aforementioned knowledge is applied to UAV field surveys to assess the high-frequency electromagnetic interference signals experienced. This is achieved using a high sensitivity (0.01 nT), scalar optically pumped magnetometer with a 1000 Hz sampling frequency. Our results indicate that adequate sensor placement and preflight evaluation of the platform-sensor interactions provide useful mitigation strategies, which can compensate for electromagnetic interference signals generated by the UAV platform during aeromagnetic surveys.