In this manuscript, the long-term behavior of piled-raft foundations (PRFs) due to the consolidation of clayey soils has been investigated by 3D finite element analysis. The validation of the numerical prototype has been carried out using the field test outcomes performed in the field laboratory and other reported results. The ultimate load capacity of the PRFs has been assessed by varying the number of piles, diameter of piles, width of raft and groundwater level. Compressive loads are provided starting from an increment of 10% of the ultimate load till the ultimate load capacity of the PRFs. Settlements of PRFs have been observed till a time period of 1 month for each increment of loading and for a period of 1 year after the ultimate load capacity has been applied. The influence of load sharing behavior, interaction effects and factor of safety on consolidation settlement of PRFs have been analyzed, and predicted expressions are suggested. Average, differential and reference settlements are evaluated. Multiple linear regression analysis is implemented for estimating consolidation settlement. The proposed design equation has been validated using an example. It is inferred that load sharing ratio increased by about 34–48%, 6–19% and 11–20% with increase in the number of piles, pile diameter and width of raft in the PRF, respectively. The reduction rate of factor of safety of PRFs is insignificant and nearly minimizes to a constant value at higher settlement magnitude. The reference settlement increases from 49 to 54% as the value of load sharing ratio decreases.