Agutaya Villa is ideal for a family or group of 4 and is located at the northern most part of the resort . It has a master bedroom with a king-sized bed which opens to the balcony facing the bay. It also has a loft with 2 full beds, a scenic bay window ideal for watching the stars at night. The family can have cozy bonding moments at the living room with floor to ceiling glass wall which allows an encumbered view of the bay. The Villa also has a huge balcony with a sitting area and an open air jacuzzi.

Busuanga Suite is the biggest single room at la Estancia. Located at the top floor of the Calamian building, this suite provides a panoramic view of the bay. Decorated with hand carved Tagbanua style decors, and with mood lights using old lanterns provide the proper ambiance that will make guests reminisce how the natives live before the advent of electric lights. This room also boasts of a large balcony, a bathroom with a tub with view of the sea.

Linapacan, Coron, Culion, Brooks Pt rooms are the King Suites. Even though they are in the same category they are all uniquely configured and decorated. However all are large rooms with king beds and a balcony facing the sea or beach. These rooms are ideal for couples.

Balabac, Bataraza, Cagayancillo, Cuyo and Araceli are the Deluxe rooms. All have balconies facing and with two queen beds each. Rated for 2 guests, but since all are big rooms they can accommodate up to 4 guests. These rooms also have good view of the bay or beach.

Aborlan and Dumaran are the Standard rooms. They are located at the lower floors. They have 2 queen beds and are also rated for 2 guests but may be able to accommodate 4. Both have balconies facing the sea. These are ideal for guests with mobility challenges.

El Nido is the only room facing the pool and the hills. It has 1 Queen bed.