Turbulent particle-laden flows in pipes can result in particle deposition leading to the formation of solid beds. The presence of such beds modifies the flow field, resulting in secondary motions in the plane of the pipe cross-section, which in turn impact particle transport. In this work turbulent pipe flows with equal mass flow rates and solid beds of height Hb = 0 (full pipe), 0.5R (three-quarter pipe), and R (half pipe) are predicted using direct numerical simulation, with the beds represented simplistically as flat surfaces. The particulate phase is one-way coupled to the flow at a volume fraction of 10−3 and particle motion is solved for using a Lagrangian point-particle approach. The Reynolds numbers computed based on bulk velocity and equivalent pipe diameter for the full, ¾ and, ½ pipes are 5,300, 5,909 and 7,494, respectively. The same particle size is used in all the simulations and their respective Stokes numbers, based on the shear timescale, are 0.5, 1.2 and 1.9, respectively. The results for flows with beds show that the fluid flow exhibits secondary vortices and an increase in the mean streamwise vorticity caused by corners in the cross-sectional plane of the pipes, with their intensity near the upper curved wall increasing with Hb. However, the upper vortices remain relative weak compared to those in lower regions of the pipes. The increase in mean streamwise vorticity in the half pipe is larger than that in the three-quarter pipe near the upper curved wall, while similar near the flat pipe floor due to the resistance of the curved wall to secondary motions. The movement of the particles in the cross-sectional plane is consistent with that of the secondary flows, but with slightly lower velocities. In regions near the wall away from the pipe corners, particle concentration in the half pipe is lower than in the three-quarter pipe, most likely due to its thinner boundary layer. This is reversed for concentration maxima near the pipe corners because of the magnitude of the secondary flows. Finally, the secondary flow changes the deposition or resuspension rate of the particles, particularly near the pipe corners, but these are always less than equivalent rates in the full pipe flow, which is likely caused by the magnitude of the wall unit.