Clathrate hydrates are non-stoichiometric, ice-like crystalline solids that can lead to plugging of crude oil pipelines. In addition, wax deposition leads to partial or complete blockage of crude oil pipelines. Crude oil is a complex hydrocarbon mixture that includes asphaltenes, aromatics, naphthenes, resins, and paraffins. Deconvoluting the effects of solid particles and surfactants that are present in crude oil on hydrate and wax formation would improve the hydrate and wax prediction strategies. A fundamental investigation using model oil was carried out to (i) deconvolute the effect of hydrophobicity of solid particles, surfactants, and water on hydrate and wax formation in water-in-oil emulsions and (ii) investigate the relationship between hydrates and wax in silica- and surfactant-stabilized water-in-oil emulsions. The results showed that the presence of silica and water did not have a significant effect on the wax appearance temperature (WAT). In addition, the amount of hydrate formation decreased with an increase in hydrophobicity of silica nanoparticles at the water oil interface. The presence of wax promoted hydrate formation in water-in-oil emulsions stabilized using either highly hydrophobic silica nanopartides or a surfactant. On the contrary, the presence of wax did not promote hydrate formation in water-in-oil emulsions stabilized using the least hydrophobic silica nanoparticles. Our data indicate that wax did not exist at the water/oil interface; therefore, wax did not serve as nucleation sites for hydrate formation. The addition of wax affected the droplet size of water-in-oil emulsions stabilized by highly hydrophobic silica nanoparticles, which, in turn, influenced hydrate formation. Also, hydrate dissociation led to destabilization of water-in-oil emulsions in the presence of wax that led to changes in the WAT.