Apparatus and method for managing data in a hybrid data storage device. In some embodiments, the storage 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 local volatile memory has separate HDD and SSD partitions respectively accessible by the HDD and SSD controller circuits. A top level controller circuit performs a cleaning operation to transfer a data set from the non-volatile solid state memory to the rotatable storage media by issuing a read command to the HDD controller circuit to retrieve the data set to the HDD partition, transferring the data set from the HDD partition to the SSD partition, and issuing a write command to the SSD controller circuit to write the data set from the SSD partition to the non-volatile solid state memory.