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I have Windows and want to install encrypted Ubuntu (Home + Swap + System) - it giving me that option during installation when I'm choosing partitions so my question is will I be able to boot both Windows and Ubuntu when I encrypt Ubuntu or will it break Dual Boot ?

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If you encrypt your Linux partitions, this has no impact on Windows. You'll need a small boot partition for the bootloader anyway, regardless of whether you run only Linux or Linux plus Windows. Select manual partitioning during the Ubuntu installation, create an encrypted container, and make three logical volumes (/, /home and swap) on it. Make a small /boot partition (80MB minimum, 200MB recommended) outside the encrypted container. Make sure to shrink, not delete, the Windows partition. The installer will automatically pick up your Windows installation and offer dual boot.

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