Single MSI to install correct 32 or 64 bit c# application

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No, this is not possible. See Heath Stewart’s Different Packages are Required for Different Processor Architectures post. The only way to handle this with MSI is with a bootstrap along the lines of what you describe. If you just needed to put a file or key or two in a 64-bit location, it’s possible (but not recommended) to do that in a custom action, but changing the target installation location and using built-in MSI file support won’t work.

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