Link first runs into Ambi's Guards when he journeys to the Past in Lynna Village. Ambi's Guards are supervising the construction of Ambi's Tower, while there are also guards blocking the entrance to Ambi's Palace.
The primary antagonist of Oracle of Ages, Veran, takes control over Nayru early on in the quest and is in need of Mystery Seeds. Veran convinces Queen Ambi to offer up a reward to anybody that finds such seeds. Ambi's Guards are ordered to find Mystery Seeds in the Deku Forest. Link journeys through the Deku Forest and acquires Mystery Seeds himself. Upon confronting one of Ambi's Guards, Link is taken to Ambi's Palace to claim his prize. In exchange for bringing Mystery Seeds, Link is awarded some Bombs, which allows him to enter the second dungeon of the game, the Wing Dungeon.
Later on in the quest, Link and Ralph need to sneak past Queen Ambi's Guards in order to reach the Possessed Nayru. After a battle with her, Veran leaves the body of Nayru and instead takes control over Queen Ambi. Veran, now acting as Queen Ambi, orders the Guards to capture Link, Ralph, and Nayru. Using Nayru's power, the trio escapes.
After fighting Veran at the end of the game, Queen Ambi summons her guards to assist in the battle. Link defeats Veran prior to the Guards arriving, but after Veran has been defeated, Ambi's Guards no longer attack Link. They view Link has a hero and Link can walk freely through Ambi's Palace.