Apparatus and method for managing data in a hybrid data storage device. In some embodiments, a hybrid device has a hard disc drive (HDD) controller circuit coupled to non-volatile rotatable storage media and a solid state drive (SSD) controller circuit coupled to non-volatile solid state memory. A top level controller circuit directs a first portion of the received access commands to the HDD controller circuit and a second portion of the received access commands to the SSD controller circuit. The top level controller circuit performs an embedded queuing operation to forward internally generated data cleaning commands to an HDD command queue to write data previously transferred from the host device to the solid state memory to the rotatable storage media concurrently while least one of the first portion of the access commands is pending in the HDD command queue.