We study the properties of dark matter haloes in a wide range of modified gravity models, namely, f(R), DGP and interacting dark energy models. We study the effects of modified gravity and dark energy on the internal properties of haloes, such as the spin and the structural parameters. We find that f(R) gravity enhances the median value of the Bullock spin parameter, but could not detect such effects for DGP and coupled dark energy. f(R) also yields a lower median sphericity and oblateness, while coupled dark energy has the opposite effect. However, these effects are very small. We then study the interaction rate of haloes in different gravity and find that only strongly coupled dark energy models enhance the interaction rate. We then quantify the enhancement of the alignment of the spins of interacting halo pairs by modified gravity. Finally, we study the alignment of the major axes of haloes with the large-scale structures. The alignment of the spins of interacting pairs of haloes in DGP and coupled dark energy models show no discrepancy with GR, while f(R) shows a weaker alignment. Strongly coupled dark energy shows a stronger alignment of the halo shape with the large-scale structures.