Gameplay in Beyond the Portals functions similarly to that of its predecessor. Players predominantly control Rallen in the field, although from time to time, they will be able to control Jeena to solve puzzles. Five planets of the Nanairo Star System, from the first game are accessible once more. At certain points in the game, portals will open that will allow the player to travel to different star systems. There are a total of ten planets and three portals spread out over four star systems. During normal gameplay, the player is given the option to play a mini-game, flying the Patrol Cruiser, whilst dodging asteroids, in order to travel through a portal that links to another star system.
At the Service Bay orbiting the planet Kollin, the player may speak to an Engineer on board to either make or attach Ship Parts. These ship parts are made up of 3 Rare Minerals, Titanium, which takes on the appearance of a stack of metal sheets, Metalium, which takes on the appearance of a Meteorite with pulsing lines strung across it, and Marble, which takes on the form of a pale blue ellipse shape. Apart from aesthetic changes, these parts also modify ship stats in the Portal mini-game. The starting ship is automatically Equipped with "Jet" parts in all 3 areas.
Rallen fights field Battles with "Krawl Dust" outside of Krawl vortexes. Rallen can use the sword and blaster to attack Krawl Dust and the glove to stun them. Each successful kill gives Rallen some experience points, and after a certain amount of experience, his rank will increase, allowing him access to more powerful equipment. Krawl Dust is spawned from Large Vortexes.
Encounter Battles are fought inside Krawl vortexes. Encounter Battles may be initiated by walking into a vortex. Once inside the vortex, the player controls the first of two offensive Spectrobes while the second is controlled by the computer. The player may switch between the two Spectrobes at any time. In order to win the battle, all of the opposing Krawl must be destroyed. Spectrobes can use a variety of attacks to fight, the most basic of which is a standard attack. The CH Gauge also makes a return from the original Spectrobes. With each successful hit, the CH Gauge fills, and when it fills to a certain point, special, more powerful attacks may be executed. Like the Spectrobes, all Krawl have an attribute of Corona, Flash, or Aurora, and their type will determine their strengths and their weaknesses. Once the battle is done, remaining Spectrobes receive a certain amount of Minergy (a contraction of Mineral Energy), and the player receives some Gura (the currency of the game) and on occasion, an item, and on a very rare occasion, a mineral.
Excavation also makes a return from the original title. Players may use a variety of tools to retrieve either a fossil, a mineral, a cube, or a mystery stone from the ground. Sometimes, players may find an invisible hexagon shaped door that allows them to enter a secret map area provided they have the correct Child Spectrobe type (Corona, Aurora, or Flash) accompanying them. In certain areas, special tools may have to be used to get past the terrain; for example, a flame thrower for ice, a water nozzle for lava, etc. Each of these drills must be used meticulously and with precision to master excavation.
In addition to the 73 original Spectrobes from the previous title, Beyond the Portals boasts 112 new Spectrobes. It also introduces a new variety of Spectrobes: "Dark Spectrobes". These Spectrobes are already existing Spectrobes afflicted with dark influence from Krawl, and are much more powerful than their normal counterparts. They boast alternate darker color schemes, featuring primarily black with colored highlights.
Unlockable devices which contain "Ultimate Spectrobes" which are not obtainable by normal means. Each Geo has the effect of destroying all the Krawl on the battlefield through a unique cut scene with each Ultimate Spectrobe. Once a Geo is equipped it will replace the effect of the CH Gauge.