We show that in pulsed electrically detected magnetic resonance (pEDMR) signal modulation in combination with a lock-in detection scheme can reduce the low- frequency noise level by one order of magnitude and in addition removes the microwave-induced non-resonant background. This is exemplarily demonstrated for spin-echomeasurements in phosphorus-doped silicon. The modulation of the signal is achieved by cycling the phase of the projection pulse used in pEDMR for the readout of the spin state.