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I have found that it is possible to run multiple instances of Skype using the /secondary key.

The second instance, however, asks to enter or select credentials, while I want it just to pick the username which have not been used by the first instance.

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up vote 4 down vote accepted

The only solution I have found and use is combining the /secondary key with the /username: key:

start /D "C:\Program Files (x86)\Skype\Phone" Skype.exe /username:user1 /secondary
start /D "C:\Program Files (x86)\Skype\Phone" Skype.exe /username:user2 /secondary

This requres pressing a button Sign me in in the second instance's welcome window. This fills in the passord automatically, however.

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If you are lazy about pressing sign in button everytime, you can add argument /password:xyz to it. It will then auto sign-in – VarunAgw Jan 4 '15 at 12:59

Maybe check out this, auto login to two accounts:

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Could you add a summary of the link? Something along the lines of: It involves making 2 new shortcuts for your 2 accounts and making a script to make sure it works... – ᔕᖺᘎᕊ May 29 '14 at 11:59

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