To clean up the MessageBox

• Stop all BizTalk services.
• Reset IIS server (run iisreset from start/run) if you are running any webservices
• Execute stored procedure bts_CleanupMsgbox on your message box database
• Execute stored procedure bts_PurgeSubscriptions on your message box database
• Restart all BizTalk services

 To clean up the Tracking data

• Stop all BizTalk services.
• Execute stored procedure dtasp_CleanHMData on your tracking database (BizTalkDTADb)
• Restart all BizTalk services

Finally shrink all databases:

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