This info is quite hard to come across and Fortigate don’t have it in their GUI from FortiOS v5.0+, SSH into your Fortigate’s CLI and enter the following (it can be done on both software aggregated and standard interfaces):

config system interface
edit [interfacename]
    set mtu-override enable
    set mtu 9208

Confirm your MTU size change has worked on the given interface by plugging directly into it (test MTU in accordance to my guide here).

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