Context. Quasi-periodic pulsations (QPP) of the electromagnetic radiation emitted in solar and stellar flares are often detected in microwave, white light, X-ray, and gamma-ray bands. Mechanisms for QPP are intensively debated in the literature. Previous studies revealed that QPP may manifest non-linear, non-stationary and, perhaps, multi-modal processes operating in flares. Aims. We study QPP of the microwave emission generated in an X3.2-class solar flare on 14 May, 2013, observed with the Nobeyama Radioheliograph (NoRH), aiming to reveal signatures of the non-linear, non-stationary, and multi-modal processes in the signal. Methods. The NoRH correlation signal obtained at the 17 GHz intensity has a clear QPP pattern. The signal was analysed with the Hilbert-Huang transform (HHT) that allows one to determine its instant amplitude and frequency, and their time variation. Results. It was established that the QPP consists of at least three well-defined intrinsic modes, with the mean periods of 15, 45, and 100 s. All the modes have quasi-harmonic behaviour with different modulation patterns. The 100 s intrinsic mode is a decaying oscillation, with the decay time of 250 s. The 15 s intrinsic mode shows a similar behaviour, with the decay time of 90 s. The 45 s mode has a wave-train behaviour. Conclusions. Dynamical properties of detected intrinsic modes indicate that the 100 s and 15 s modes are likely to be associated with fundamental kink and sausage modes of the flaring loop, respectively. The 100 s oscillation could also be caused by the fundamental longitudinal mode, while this interpretation requires the plasma temperature of about 30 million K and hence is not likely. The 45 s mode could be the second standing harmonics of the kink mode.