A method and system are disclosed for controlling the storage of data in a storage device to reduce fragmentation. The method may include a controller of a storage device receiving data for storage in non-volatile memory, proactively preventing fragmentation by only writing an amount of sequentially addressed logical groups of data into a main storage area of the storage device, such as multi-level cell (MLC) flash memory, and reactively defragmenting data previously written into the MLC memory when a trigger event is reached. The system may include a storage device with a controller configured to perform the method noted above, where the thresholds for minimum sequential writes into MLC, and for scanning the memory for fragmented data and removing fragmentation by re-writing the fragmented data already in MLC into new MLC blocks, may be fixed or variable.