Rune Factory Frontier has multiple dungeons and bosses in the game that each introduce new challenges, but also new rewards.
There are four dungeons in Rune Factory Frontier. Each dungeon has different parts, floors, puzzles and monsters.
 Green Ruins
The first Ruins you finish. The season here is always spring, so it's the perfect place to grow spring crops. You can open this dungeon by using the sickle form Erik to cut the weeds blocking your path.
Monsters are in a very low level in this dungeon, as it's for beginners. The main puzzle is that the dungeon is a like a maze, and there are vines in your way to slow you down. A simple and straight-forward dungeon. The recommended level to complete this dungeon is 10-20.
 Lava Ruins
The second dungeon in the game. To unlock this, you must have kept a good population of runeys in the area, to make the tree grow bigger. You will then need a Tree rune stone to place in the hole of the tree to make it tall enough to push open the way to the Lava Ruins. It's always summer in this dungeon.
Monsters are in a fair level here, and the dungeon's puzzles include bombs, floors with hot lava, manipulating boulders, tossing bombs and piles of rubble that constantly block your path. An intermediate dungeon. The recommended level to complete this dungeon is 40-50.
 Snow Ruins
The third dungeon in the game. To unlock this, you must have first defeated the boss in the Lava Ruins and placed the Relic it drops on the stone tablet beside the library. This is the dungeon where the season stays autumn.
Monsters are in a high level here, so come prepared. Puzzles include ice machines that harm you, things to break in order to open doors, maze-like structure and many monsters in an area. A dungeon for those who are in a high level. The recommended level to finish this is 70-80.
 Whale IslandLute, the peddler, and he'll tell you about a sprout growing there. Whale Island is an all-seasonal dungeon; you can grow any crop here.
Monsters are of every level on Whale Island. It gets much tougher as you progress. The puzzles include poisonous areas, many monsters in one place, a maze-like structure and doors that require Rune Stones to open. An all-around dungeon. The recommended level to finish this is 80-100.
There are several Bosses in Rune Factory Frontier. There is always a purple HP bar in the bottom of the screen when you're fighting them. Also, there is a boss room, a large area where the fight takes place.
 First Boss
 Second Boss
The Lava Ruins Boss is the one Kanno warned you about, that it changes shapes. It first appears as a swarm of eight bees with machine gun like stingers. Use your icifier sword doing the special attack move to kill several of these at once. The Lava Ruins is the dungeon where the season is always summer.
Once you have removed the bees four large panthers will appear. Attack the one on the end first, attacking one at a time. They have three basic moves, all of which are easy to dodge. Keep away from its claws and breath. Run in, attack, run out. They move in a pattern, and once you learn the pattern you can take these down easily.
Next come the giant trolls. These giants move very slowly and repeat the same movements over and over. They are the easiest to elliminate. Watch for when they throw themselves down, then run up to them and attack. When they are gone, be prepared for about 16 slimes. There is a crack on the floor. Get all the slimes to chase you as a group and then guide them over to the crack. Once they are all on one side of the crack they will no longer chase you around the room but try and get you over the crack, which they cannot do. You, however, can get them if you have a spear or lance. Keep poking at them until they are all dead.
Finally we get to the actual boss with the energy bar showing at the bottom of the screen. Stay out of his way. He shoots fire at you, he explodes the area around himself, and he will jump on top of you. He will blow bombs at you. He always shoots four bombs. Run around him while he's shooting the bombs, and after the fourth bomb, you can go in for one or two hits. The tomahawk does up to 150 damage with each hit. Then get out of the way again. This boss drops food, the Relic needed to unlock the Snow Ruins, and a red core.
 Third Boss
Another boss is Brodik. There are two parts to this battle. Luckily, the Golem and Brodik don't flash red and power-up once they've almost been defeated.
In the first part of this boss battle, Brodik sends a Golem to attack you. The best way to defeat the Golem is to have a monster distract it with attacks, then use a special attack from your sword or magic to dish out damage. For spells, the Hell Branch is a good weapon to use. The platform is smaller than the other boss arenas, so the Golem is more likely to get hit by your Hell Branch's spells.
In the second and final part of the battle, it's Brodik himself who faces you. This part of the battle occurs the next day, at the same place. The easiest way to beat Brodik is to attack after he attacks. Some long-range monsters would work best, like a Mamoo. His attacks consist of spinning ones, where he lunges at you, dealing lots of damage. Fortunately, this move is easy to avoid. His other moves consist of swift slashes, so be careful not to get wrapped up in one of his combos. He dodges most of the time, so getting a clear shot that will hit is tough to get at first. The best time to attack is right after he does a spinning lunge; just sneak up behind him and attack, then dodge again.
 Fourth Boss
The fourth boss is Iris Noir, in the third level of the Snow ruins. She floats and teleports around the room, constantly attacking you and warping when you get too close. It's impossible to harm Iris; she has a barrier surrounding her. You must destroy the four machines around the room with blue orbs in order to defeat Iris Noir. She has a wide range of attacks, and they can easily reach you where ever you are. The trick is to dodge her spells, then attack the orbs. It's helpful to have a monster along to distract her while you fight the machines. The machines won't retaliate or move; the best way is to cast a spell like eruption to attack the machine several times while you dodge and move to the next one. Once all the machines with the blue orbs are defeated, Iris will faint, and Raguna will be found back in his bed.
However, if you have Iris Blanche at 4 love points, you won't have to fight her.
 Fifth Boss
Fighting Gelwein requires patience and skill. Just before fighting Gelwien you must fight the magical creature. He shoots out tail stingers, and this is the best time to attack him. After you defeat him, Gelwein joins the magical creature. Gelwein will send monsters at you to help him. He uses magic as well. If you hide behind the monsters they will take the damage meant for you by Gelwein. Your mission is to stay alive as long as he has the runes helping him. When the maidens come to your aid, you can now fight Gelwien and win. Run up to him when he's using his magic and use your special attacks on him.
 Sixth Boss
The Snow Ruins has a snake that has dangerous breath. You can take your tamed monster in with you and leave him in the hallway until the snake attacks speed up. When you want him to help you, just go down the hall and get him. He will follow you. Hide behind the walls while the snake blows cold air on you. At your first chance, run out of the hall and then dodge quickly back in. He will move his head down and then spray a blast of cold air to the left and to the right. You can attack him in his nose a couple of times with a one handed sword. Then run back into the hallway. He crawls out of his hole and you will have a chance to do some real damage by hitting him on the tail. This boss takes a long time and lots of patience. He drops snake tongue, food, gem or crystal, and platinum.
 Final Boss
At the top of Whale Island lives a giant jellyfish. You'll need to be at a higher level to beat him and to take plenty of medicines and food. The best strategy is stay out of the way and attack his smaller, pink-tipped tentacles. When all of his tentacles are up, he will become dizzy. You can get in eight hits before he wakes up, however, if you need to eat or drink, hit him four times, move to safety, and quickly eat. right before he is almost dead he speeds up and becomes more difficult to kill. His tentacles will come back to life faster too. This is the stage where having a lot of energy drinks ready to go will greatly help. He drops platinum, bright tentacles, and food. After you defeat him, the whale leaves you a small crystal as a thank you gift.