So it looks I can change the background-color of an empty md-checkbox by doing :
md-checkbox .md-icon {
background: red;
}
But I can't manage to change the background of a checked md-checkbox.
I tried  to play with :checked, ::before, ::after... But didn't succeed.
How should I proceed ?
You need to use theme class as well as md-checked class combination in order to define selector with higher specificity. For example:
md-checkbox .md-icon {
    background: red;
}
md-checkbox.md-default-theme.md-checked .md-icon {
    background: orange;
}
And of course, avoid using !important, this is a sign that something is wrong with your styles.
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