To enable user diversity and multiplexing gains, a fully digital precoding multiple input multiple output (MIMO) architecture is typically applied. However, a large number of radio frequency (RF) chains make the system unrealistic to low-cost communications. Therefore, a practical three-stage hybrid analogue-digital precoding architecture, occupying fewer RF chains, is proposed aiming for a non-orthogonal IoT signal in low-cost multiuser MIMO systems. The non-orthogonal waveform can flexibly save spectral resources for massive devices connections or improve data rate without consuming extra spectral resources. The hybrid precoding is divided into three stages including analogue-domain, digital-domain and waveform-domain. A codebook based beam selection simplifies the analogue-domain beamforming via phase-only tuning. Digital-domain precoding can fine-tune the codebook shaped beam and resolve multiuser interference in terms of both signal amplitude and phase. In the end, the waveform-domain precoding manages the self-created inter carrier interference (ICI) of the non-orthogonal signal. This work designs over-the-air signal transmission experiments for fully digital and hybrid precoding systems on software defined radio (SDR) devices. Results reveal that waveform precoding accuracy can be enhanced by hybrid precoding. Compared to a transmitter with the same RF chain resources, hybrid precoding significantly outperforms fully digital precoding by up to 15.6 dB error vector magnitude (EVM) gain. A fully digital system with the same number of antennas clearly requires more RF chains and therefore is low power-, space- and cost- efficient. Therefore, the proposed three-stage hybrid precoding is a quite suitable solution to non-orthogonal IoT applications.