I've tried many methods of tuning
Such as natural harmonics, normal 5th fret, a analogue tuner,
but whenever I play a chord, it doesn't sound clean at all.

Its a Martin d-18

The intonation might be off, I've had quite a few instruments with that problem.
My Gear:
Gibson Faded Flying V
"Dante's Inferno" Iceman
Fender Hot Rod Deluxe 112

Quote by freedoms_stain
I can't imagine anything worse than shagging to Mark Knopfler.

Maybe shagging Mark Knopfler, but that's about it.
it the guitar sounds to be in tune when unfretted, but sounds off when you play chords or notes, chances are it's an intonation problem.
Quote by Skeet UK
I just looked in my Oxford English Dictionary and under "Acoustic Guitar", there was your Avatar and an email address!
Use the tuner to check the strings in open mode. Then check each string while fretting it at 12. It should show the same as open on the tuner. If not, then you'll have to adjust the saddle on the bridge for that string.

There should be a screw to move the saddle forward and back. Not up and down. Loosen the string, adjust the screw about 1/4 turn. Re-tune and recheck. You might have to go the other way depending on which way it is off. This might help. Could be a neck adjustment too.

If you are unsure or unhappy about messing with it, I suggest you take it to a shop and have it set up. Might cost a few bucks but hopefully you'll get it fixed
I think it might be an intonation problem, also its not an electric guitar so I can't change the intonation myself. How often should one get their guitar set up? Thanks
How fresh are the strings that are currently on it? If old, they may be throwing the intonation off.
It's unusual for a quality guitar to have really severe intonation problems..... More often the problem is due to high action (which makes the strings "go sharp" when they are pulled down to the fretboard), bad/worn strings, or humidity-induced warping which can cause much the same effect as high action.
If the intonation is really off, then about all you can do with most acoustics is "compensate" the saddle by cutting it away so that the string length is either shorter or longer... Naturally this is limited by the width of the saddle.
In really severe cases, a new saddle slot might have to be cut and the old one filled in, or the saddle "split" so that you have two saddles..... Usually you don't see anything that bad with a modern-production instrument.