Electric Blob Queen is fought in a similar manner to Electric Blob King, except her battle is slightly different and more difficult. She will appear in a pool of water and float along its surface. The pool is deep in the center, while shallow near the edges. Like the former BlobBoss, the Blob Queen will fire three blasts of electricity. The electricity will travel in the water and electrocute any Link standing inside, as indicated when the water flashes pink. The grassy ground is safer, provided that the Links avoid the blasts. The Blob Queen's weak point is the red core inside her gelatinous body, which can be shot with the Bow. The Blob Queen will occasionally twirl around as she is being attacked, which will momentarily protect her from the onslaught of Arrows and force the Links to realign their shots. After she is damaged enough, the Blob Queen will then submerge underwater, requiring that the Links force her out with the Water Rod.
Once she is forced out of water, the Electric Blob Queen will grow in height, leaving her red core out of reach. As before, the Links must form a Totem of two to reach her height and shoot at the core. The Blob Queen will continue to fire electric blasts, although her attack can be interrupted by shooting her core. The Blob Queen will then grow to full height, requiring the Links to form a Totem of three or stand atop the Water Rod's pillars. After inflicting more damage, she will then force her red core through her head, putting it out of reach for even three of the Links. To hit the core, two of the Links must form a Totem on top of one of the wooden platforms or a water pillar. She will be defeated after a few more hits.