At the north eastern corner of Khendjer's pyramid complex is a small subsidiary pyramid, which is thought to have been prepared for the burials of two of Khendjer's queens. G. Jequier also found shaft tombs nearby, which may have been prepared for other royal family members. The entrance to the substructures of this pyramid lie at the base of its eastern base. A small stairway leads to two portcullis chambers similar to those found in the main pyramid. Here too the portcullises were left open. Beyond is an antechamber branching to the north and south to two burial chambers lined with masonry and both housing a large quartzite coffer. The lids of the coffers were found propped on blocks as they should be before any burial. The two coffers were thus most probably never lowered into place and put into use.
Some unexpected turn of events probably prevented their use, although there is nothing directly suggesting that the king wasn't interred as planned in the main pyramid. Interestingly however, in a recent study of the Second Intermediate Period, egyptologist Kim Ryholt concludes that Khendjer's successor, Imyremeshaw, usurped the throne.