In Mario & Luigi: Bowser's Inside Story and its remake, Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey, while looking for a seat in the Fawful Theater, a Shroob can be seen in a seat on the lower right-hand corner. If Bowser tries to speak to it, it stares blankly without saying anything. Much later in the game, a group of three Shroobs appears as an optional boss. They are found in the preservation room in Bowser's Castle, which needs a password to be accessed. The password of the cold room is □, □, ○, △, △, △, followed by hitting the switch on the door itself, with signposts that are found in Bowser's Castle hinting at what the password is. Once inside, the Bros. must hit a red switch that causes three of the Shroobs to thaw. As Mario and Luigi begin to explain their history to Starlow, the three Shroobs wake up and attack the brothers.
They have two attacks that were very similar to the ones (especially the Guardian Shroobs) they used in Mario & Luigi: Partners in Time. For the first, the attacker will flag down a companion, and they will each shoot a laser at Mario and Luigi. The other attack is a simple laser blast, delivered to only one brother. Before executing this attack, the attacker will always pirouette; in Mario & Luigi: Partners in Time, they would pirouette only before attacking Luigi, and spark before attacking Mario. Here, the brother being targeted is indicated by the spin's direction: a Shroob spins clockwise to attack Mario, and counterclockwise to attack Luigi. In the remake, each of the Shroobs gain the Fury status after losing half their HP, like other bosses, and will fire lasers much faster.
Various other Shroobs are visible in the background of the battle, including broken Shroids, Junior Shrooboids, Shrooba Divers, Commander Shroobs and even Elder Princess Shroob; in the remake, a frozen Princess Shroob can now be seen alongside Elder Princess Shroob. Also, if a player uses the Jump Helmet attack, a single RC Shroober is seen as Mario and Luigi walk back in order to commence the attack.
After defeating them, Mario and Luigi receive all ten Attack Pieces for the Magic Window Special Attack. They also receive the Shroob Boots, which may lower the attack power of stomped enemies. Starlow then compliments Mario on stopping the invasion as a baby; when he explains that Luigi fought hard as well, Starlow sarcastically remarks that he did so by "ferociously crying", referencing the baby tears that were ultimately the aliens' downfall. When she learns that it was indeed Luigi who ultimately trumped the Shroobs, she apologizes to him and calls him "super". Despite being bosses, the Shroobs use the same death animation as normal enemies; this also occurs with Bowser Memory ML.
The Shroobs, along with the Elite Goombule and Bowser X, were not in the Prima Guide Enemy Compendium; however, the Shroobs were mentioned in the walkthrough.
In addition to reprising their roles in Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey, multiple Shroobs appear as ranged enemies in the Bowser Jr.'s Journey mode, where they attack using their Shroob Blasters and are weak to Swoops. The Shroobs battle Bowser Jr. in Chilling Magma after he, Kamek, and Morton go into the basement of Bowser's Castle to retrieve Ever Ice. After the Shroobs are defeated, Bowser Jr. is able to collect the Ever Ice. Several Shroobs also appear in later missions such as The Lost Alien, The Power of the Koopalings and The Best Beast, with some under the effects of Malatone Formula:X.