If you are using fpdf, in order to be able to use line breaks you will need to use a multi-line text cell as described here.
If you use this, then line breaks in your text should be interpreted and converted correctly.
Just a quick example:
$pdf->Multicell(0,2,"This is a multi-line text string\nNew line\nNew line");
Here, 2 is the height of the multi-line text box. I don’t know what units that’s measured in or if you can just set it to 0 and ignore it. Perhaps try it with a large number if at first it doesn’t work.