Doing a sidequest for certain persons gives you a set of 5 gratitude crystals, however, there are also single gratitude crystals laying around.
How many of those single gratitude crystals are there exactly, and where are they located?
Note that I’m not interested in the gratitude crystals you get from the sidequests, only those that are laying around.
There are 15.
From this guide:
Individual Gratitude Crystals (15 Gratitude Crystals)
NOTE: There are 15 individual gratitude crystals that can only be
found at night time. Since you cannot fly around on your Loftwing
during the nighttime, these gratitude crystals can only be collected
at locations that have beds where you can go to sleep. Once you obtain
the Master Sword, you can gain the ability to dowse for Gratitude
Crystals. You can also grab these crystals using the beetle.
- Found within Link’s Room on the desk.
- On the second floor of the Knight Academy, there is a Gratitude Crystal at the north part of the hallway.
- Inside of the Sparring Hall, there is a Gratitude Crystal up in the raftors. You will need to have the Beetle in order to get this
- Just south of the Knight Academy and down the steps, you’ll find a windmill. There is small opening here and you can climb down the vines
to get the Gratitude Crystal.
- Inside of Parrow and Orielle’s house just south of the Bazaar. The crystal can be found at the corner of the room.
- Just north of the Bazaar at the lower lever where there are wooden planks. The Gratitude Crystal is nearby.
- A crystal can be found at the base of the Light Tower at the south end of Skyloft.
- Go through the Waterfall Cave and once you reach the exit, you’ll find the Gratitude Crystal just to the left of the Bird Statue.
- Right next to the previous crystal, this one can be found in the small cavern where Link’s Loftwing was being held at the beginning of
- Near a bush and tree by the large pumpkin patch at the east end of Skyloft.
- The large waterfall at the northeast part of Skyloft has a Gratitude Crystal. You’ll need either the Clawshots to climb up or you’ll ned
the Quick Beetle to reach this Gratitude Crystal.
- Grapple up to the chimney located above the Knight Academy. You can sneak into Zelda’s room where you will find the Gratitude Crystal.
- A Gratitude Crystal can be found within the storage shed on the Pumpkin Landing.
- A crystal can be easily found on the second floor of the Lumpy Pumpkin at night time.
- Fall asleep using the bed that is on Beetle’s Air Shop. You will awaken on Beetle Island. Go outside and there is gratitude crystal at
the top of Beetle’s ship. You can use the beetle to snag this