SUMMARY Inconsistencies between (lightweight optical pumped) magnetometers in total field gradiometer surveys can introduce instrument-dependent responses, complicating geological interpretation. Here, we present an equivalent source-based processing method that combines equivalent sources with kernel regression to eliminate these instrument-dependent responses. We evaluate the method using a drone-borne triangular gradiometer survey from Rånbogen, Arctic Norway. The Rånbogen survey exhibits instrument-dependent responses in the measured total field differences, likely resulting from differences in the magnetometer’s heading error and the complexities from the induced field from the system itself. A synthetic gradiometer survey was generated to test the method, where different nonlinear synthetic heading errors were added to the synthetic magnetometer readings. The equivalent source-based processing method effectively removed these heading errors while constructing an equivalent source model that fits the actual underlying synthetic model. Furthermore, applying the method to the Rånbogen survey removes the data’s correlation to its orientation, thereby minimizing the effect of the instrument-dependent response. The method condenses the gradiometer data to a single equivalent source surface where the derivatives of the total field can be calculated to facilitate interpretation. The results suggest that the equivalent source-based method removes the inconsistencies between the magnetometers in a total field gradiometer survey, allowing for drone-borne gradiometer systems with multiple lightweight magnetometers.