Encryption changes data or information that is normally plaintext through the usage of an algorithm so that someone must possess certain knowledge to access it. This special knowledge is normally called a key. For example, something is encrypted if someone must enter a password to access it. Encrypted QR codes are QR codes that not everyone can scan and access. They are not very common, since most QR codes are used in marketing, and the developers of those codes want them to be accessible by everyone. Secure QR codes can be made that make the scanner enter a password to be able to access the content. This is a good idea to make for employees of a company. The company can make secure QR codes that the employee has to enter the company password to view. This means people outside of the company cannot see decode the QR code without the password. One Android app can encrypt and decrypt QR codes using the DES algorithm. The immigration department of Japan has used encrypted QR codes on visas.
QR codes are normally encoded in plaintext. A QR code must contain certain parts to be easily decoded. This article, Anatomy of a QR Code, breaks down the different parts of a QR code. There must be the four main squares that you can see in a QR code, two in the upper corners, one in the lower left corner, and a smaller one near the lower right corner, which contains information on the alignment pattern. There also must be white space around the outside of the QR code. This is called the quiet zone. Check out the article above to learn more about parts of the QR code.