I have inherited a production 2016 SQL Server with SSIS installed, which has many SSIS packages deployed to msdb (mostly warehouse ETL workloads that run nightly).

I would like create a new Integration Services Catalog and deploy future SSIS projects to SSISDB. Can these two deployment methods and package locations coexist? In other words, if I create the new catalog and start using the project deployment model for new SSIS projects, will that have any effect on the dtsx packages already in msdb?

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Yes, you can use both the Package Deployment Model (msdb) and the Project Deployment Model (SSISDB) in tandem with no ill-effects.

As a consultant, if I walked into a place that had both, it'd indicate that they've been using SSIS before the 2012 release and there's been no reason to upgrade existing work to a new model. In heavily regulated industries, going through the bureaucracy just to make your life easier often isn't a consideration. That or someone had a very good reason for using the legacy/msdb.

A lot of "design sins" (lack of configuration, lack of logging) in the Package Deployment Model aren't a concern with the Project Deployment Mode (logging is automatic and connection managers are easily externally configurable). The Project Deployment Model also makes parent/child design patterns more easily implemented.

From a management perspective, that's the real beauty of the SSISDB. If you want to run a package, you call the native procedures and it spins up dtexec. For packages in msdb, you are looking at either an xp_cmdshell call or a SQL Agent job as there's no native way to run them.

Backup and recovery of an SSISDB is a touch more complex due to key management but it's documented.

Deployment of packages uses two different mechanisms (dtutil vs isdeploymentwizard/managed object model/bulk insert)

Execution uses the same executable: dtexec

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