This is a port, combining 2 guides made for the original game.
Credit goes to the creators Daniël and bootski.

Achievements which can be obtained by just playing through (or are very obvious) are NOT included.

Complete the game in New Game Plus.
After beating the game once, it unlocks a new game mode (New Game Plus). You need to beat the game again on this achievement to unlock this one. The differences in New Game Plus are substantial: you no longer see the sound circles to know how much noise you're making and your vision is more lifelike, meaning you don't see behind or above you, without looking. It's a bit more difficult, but not much so.

Earn three stars in every level.
You need to acquire three stars in all levels. This is actually not too hard to accomplish. The key is sticking to one type of gameplay, either stealth or attack. Meaning, don't sneak past half the guards but kill the other half. If you kill one guard, it's better to try to kill them all in the most creative ways, since you lose the point bonus for No Guards killed (awarded at the end of the level). You should also play through trying to not ever raise the alarms as it's a -800 point deduction in game and a loss of the 3000 point bonus (total -3800 for a single raised alarm).

The best (highest points) ways to kill are Hangman's Hym, Prowling Spider (dragging them into a vent when you're in it) and (my favorite) Friendly Fire. Hiding bodies also provides a nice point addition. Killing an elite guard is 800 points.

Earn all three seals in every level.
Each level has three tasks that need to be accomplished. They are shown on the right of the map screen. Complete all three tasks in every level to unlock Perfection.

Find all three scrolls in every level.
Each level has three hidden scrolls, find all three in each level to unlock Haiku. Since finding these scrolls gives honor, which is used to unlock other special moves, not finding every scroll means that you can't unlock every special move (another achievement).

There are quite a few guides out there on the location of every scroll. I found it easier to simply use the map and leave no areas undiscovered.

Earn all of the upgrades.
Unlock all upgrades to get Marked achievement. To earn all the honor that you need to unlock all upgrades, you need to complete all seals (3 tasks), 3 stars (points) and find all hidden scrolls in every level. This makes Marked the hardest achievement to unlock in this game as in order to complete it, you must have completed the game fully (at least once).

Complete a level without killing any guards.
Do not kill any guard (no traps, tools, indirect, friendly fire, etc) to unlock Mercy. Easiest done on the first few levels. In the later levels, although it's possible, it becomes increasingly harder to complete without killing a single guard.

Complete a level without getting detected.
You get this achievement if you manage to beat a level, without getting detected once. All you have to do is avoid getting seen by any guards, which is a piece of cake if you try to avoid them alltogether. If you don't let them hear you (by running near them), don't get in their vision and avoid light, you should have little trouble getting this achievement. Especially on the easier levels.

Complete a level without killing any guards and without being detected.
This achievement is easiest done when doing the Mercy achievement. Do not kill any guard or get detected to unlock Ghost. Pretty easy in the first few levels.

Complete all of the challenge rooms.
In each level there is one scroll hidden in a challenge room, except level one. The challenge rooms are big puzzle rooms set separately (in your mind?) from the game level. They basically all are lever flipping/jumping puzzles, some harder than others. Complete all challenge rooms (11 total I believe) to unlock.
https://youtu.be/THPCYOouT1k

Terrorize 10 guards.
The easiest way I found to terrorize guards is either using the Poison Darts (unlocked attack item) or having guards find their colleagues hanging (a technique unlock)

Distract 25 guards using your equipment.
If you don't play the stealth game, Manipulator will require some doing. It involves distracting 25 guards using YOUR equipment. I completed this on my New Game Plus playthrough by equipping the Path of Silence costume (which lets you carry two distraction items) and and using the noisemakers and the flares.
You can also farm it in 'A Change in Course', throw some firecracker to the first guard and restart.

Distract 25 guards using environmental objects.
To beat the trickster achievement you have to distract 25 guards using environmental objectives. The most common way to do this is by breaking lights using your bamboo darts. The sound that it emits will distract the guards. You can see if the sound waves will actually reach them by selecting a light in aiming mode and by looking if the blue circle surrounding it reaches the guard.
Another way to distract guards is by hitting gongs instead of light, which requires the same tactic as with lights.

Perform five different types of stealth kills in one level.
In order to get Crimson Haiku, it's best that you unlock most, if not all, available stealth kills.Possible stealth kill combinations available in most levels are:

Silent Assassin; the regular stealth kill.
Bat's Prey; jumping upon an enemy and killing them before you land.
Emperor's Abyss; dragging a guard down from a vent.
Twilight Gate; kill a guard standing near a door, from the other side.
Hangman's Hymn; use your grappling hook to tumble down and kill the guard when near enough.

Kill a guard from inside the box.
Inner Heaven requires a couple equipment unlocks. First, you need to unlock the "cardboard box" distraction item, then it's upgrade which allows you to kill from inside the box. Equip the Box in your setup. When in game, wait until a patrolling guard is walking away from you, setup the box and wait. As he walks back past you, you'll get the kill prompt. Take it and you'll unlock Inner Heaven.

Get the Undetected bonus 10 times in one level.
Get the Undetected bonus 10 times in one level. To get the bonus, you need to be hidden close to a guard as they walk past. Examples are hiding behind vases and doors, inside the little alley cutouts, behind garbage bins, in dumpsters, hanging from the roof close to their heads and also lowering yourself with the grappling hook to close to their head will trigger it.

Throw the body of one guard to terrorize another.
Throw the body of one guard to terrorize another. To do this, I found it easiest to kill one guard and throw him to hit another guard who's facing the opposite direction. When he hits him, the other guard will turn around and be terrorized. Remember to jump out of the way as when he turn's around he'll be looking right at you. If he spots you before the body, he will not be terrorized. Also, if you throw the body and he doesn't detect it right away but walks up to it and discovers it like that, he will not be terrorized and he'll sound an alarm.

Within a single Focus, aim and throw three different types of items.
Throw three items in a single Focus to unlock. I will explain how to do this step by step (on a computer using mouse/keyboard). Start any level (except level 1 or 12), equip the Path of Silence costume, firecrackers (distraction 1) and flares (distraction 2). Any two throwable items will work.
Find a spot to jump from (a little bit off the ground) where you can see a guard (ideally he's facing the other way). Make sure your bamboo dart is the selected equipment. Jump off and immediately press LCtrl AND HOLD IT (starts Focus which slows down time). Click on the guard to throw the dart, press 2 and throw item 2 (firecracker), press 3 and throw item 3(flare). Only then can you release LCtrl. All three items will be thrown at once and you'll have the unlock.

Stealth kill an elite guard after stunning him.
At level eight, you can get this achievement by stunning an Elite guard. The method adviced by the game is pulling the lever activating the electric wires when he walks by. If you do this correctly, it's an easy kill.

Stealth kill a guard from inside a dumpster.
Kill a guard from inside a dumpster. This technique needs to be unlocked. It's available later in the game which is fine as that's when you start seeing dumpsters. Hide in a dumpster along a patrol route and when the guard walks by you'll see the kill prompt. When you kill him, you automatically leave his body in the dumpster and jump out.

Kill a guard by getting other guards to shoot him.
In order to get this achievement you will need to terrorize a guard. You can do this most easily by throwing a guard you have already killed at your next victim. He will then start shooting aimlessly. The achievement is earned if he shoots one of his allies. You will also get 700 points for 'Friendly Fire'.

Terrify a guard and cause him to stumble to his death.
Terrorize a guard and make him fall to his death. This one is a little bit hard to achieve as it requires both a guard on an edge AND something to terrorize him with. Personally, I used a thrown body at a sniper and he stumbled off backwards. Here's a little video guide that show's both how to throw a body to terrorize and make some fall to their death.
https://youtu.be/VyFDfsaAGks

Terrify a guard with a hanging stealth kill five times.
Terrify guards using hanging bodies 5 times. Two guards are necessary each time obviously (1 to kill, 1 to scare). Kill gaurd one, and hang him from a perch point (either using Hangman's Hymn or the other unlock that lets you hang bodies from perch points). Then sit on top of the perch point and shoot guard 2 with a bamboo dart. Then hide. He will look up to where you were when you shot him and see his buddy hanging there and get terrorized. Complete this 5 times to unlock Gallows.

Use a dead body to lure another guard and then stealth kill him.
To gain this achievement you need to lure another guard into a kill by using a dead body. A good way to do this is by killing a guard, leaving it be and wait for another guard to come near. If you are able to hide somewhere above the dead body, you can use the Bat's Prey stealth kill to jump upon a guard if he comes near the dead body. Make sure the dead body is in a position where another guards flashlight will cross over it. This is easiest to do when the guard you plan on luring walks a path, so you can place the dead body there when he walks the other way and get into position before he turns around.

Stun an elite guard with moths then dispatch him.
https://youtu.be/yGfykReTyJ0

Knock out an enemy again that was revived from being knocked out.
Can be obtained in level 3 - The Trail of Shadow, after playing the DLC level and obtaining the Path of Wisdom. Knock the first guard out, lure the second one in with a bamboo dart and hide until they are both back on their positions, then knock out the first guard again.

Dispatch two enemies at once using a body infected with Toxic Fungus.
Dispatch two enemies at once using a body infected with Toxic Fungus. This is done very close to the beginning of Level 9 (A Blade at his Neck).
https://youtu.be/wu-iUHR0gjY

Read one of the history lesson developer commentaries.
Enable the developer commentaries in the game-options.
Go to the level 'A Change in Course' in Oshi City. Click the first bubble you find.

Disable a spotlight using the Dusk Moths.
https://youtu.be/5syzAdjNQY8