The majority of covers clamp on, so it really depends on what kind of bed liner you have. Under-the-rail liners generally don’t interfere with where the cover clamps go, so you shouldn’t have a problem with these (one exception may be retractable covers in the bulkhead area). Over-the-rail liners may present you with some installation challenges, however. Because these may cover over some clamping areas, you might need to do some drilling or cutting to securely attach the cover to the bed with this type of liner.