The vibration dynamics of relatively large granular grains is extensively treated in the literature, but comparable studies on the self-assembly of smaller agitated beads are lacking. In this work, we investigate how the particle properties and the properties of the underlying substrate surface affect the dynamics and self-organization of horizontally agitated monodisperse microspheres with diameters between 3 and 10 μm. Upon agitation, the agglomerated hydrophilic silica particles locally leave traces of particle monolayers as they move across the flat uncoated and fluorocarbon-coated silicon substrates. However, on the micromachined silicon tray with relatively large surface roughness, the agitated silica agglomerates form segregated bands reminiscent of earlier studies on granular suspensions or Faraday heaps. On the other hand, the less agglomerated hydrophobic polystyrene particles form densely occupied monolayer arrangements regardless of the underlying substrate. We explain the observations by considering the relevant adhesion and friction forces between particles and underlying substrates as well as those among the particles themselves. Interestingly, for both types of microspheres, large areas of the fluorocarbon-coated substrates are covered with densely occupied particle monolayers. By qualitatively examining the morphology of the self-organized particle monolayers using the Voronoi approach, it is understood that these monolayers are highly disordered, i.e., multiple symmetries coexist in the self-organized monolayers. However, more structured symmetries are identified in the monolayers of the agitated polystyrene microspheres on all the substrates, albeit not all precisely positioned on a hexagonal lattice. On the other hand, both the silica and polystyrene monolayers on the bare silicon substrates transition into less disordered structures as time progresses. Using Kelvin probe force microscopy measurements, we show that due to the tribocharging phenomenon, the formation of particle monolayers is promoted on the fluorocarbon surface, i.e., a local electrostatic attraction exists between the particle and the substrate.