The effect of the density of active molecules in molecular junctions (MJs) has been investigated by using a host/guest strategy. Mixed layers consisting of oligothiophene (BTB) encapsulated by β-cyclodextrin (BTB@β-CD) were generated. Cyclodextrins were then removed, and the pinholes generated were filled with BTB to obtain BTB@BTB films. MJs based on mixed BTB@β-CD and BTB@BTB layers, as well as single-component BTB MJs, were compared. The variation of ln J vs thickness is similar for all systems while the J o of BTB@β-CD MJs is 20 times lower than that of BTB MJs. After β-cyclodextrin has been removed, and the pinholes filled, J o increases and reaches the same value as for the BTB MJs, showing that the conductance scales with the number of active molecules. This strategy provides a unique method for investigating molecular interactions in direct tunneling MJs as well as the possibility of fabricating new functionalized MJs based on mixed layers.