Are you saving out a low resolution pdf? If a logo is not a vector format, Acrobat sees it as an image, when you save out to a low resolution pdf it will reduce the quality of the image to save the file size of the ppf down. Try saving the pdf as high quality. If it looks fine there, than you have found the issue.
Hi. Thanks for stepping in with some advice. I'm actually exporting at print quality so avoiding the low resolution pdf issue but the logo has a transparent background and is a png file. Would it help if I resaved it as a vector file? Any further advice would be welcome. It looks 100% fine in Indesign but just my exporting to PDF makes the logo look terrible. Thanks again..
A logo should alway be in vector, best as ai file or pdf.
But it will not help to save a png as vector, you should take the original vector file and place in InDesign.
png is also a rib only file type without colormangement, I suppose for print you might at least need a cmyk logo file.