- Upgrading the Fossil Chip allows the player to dig up new Fossil Rocks. The cost of an upgrade is 10,000G for the Fossil Chip 1 and 35,000G for the Fossil Chip 2.
- Upgrading the Fossil Filter decreases the chance of digging up normal rocks.
- Filter 1 costs 5000G
- Filter 2 costs 8000G and removes any chance of digging up normal rocks.
- Upgrading the Monitor increases the size of the display and the detection range of the sonar, meaning more fossils can be seen with each scan.
- Monitor Upgrade 1 is 800G.
- Monitor Upgrade 2 is 3500G
It can also be upgraded by progressing through the storymode, allowing the detection of objects such as Caliosteo Slablets and Sub-Idolcomp pieces. These upgrades are free of charge.
In Fossil Fighters: Champions, the sonar may show yellow blips during normal digging, signfying a rare fossil rock. The case of the sonar changes when it is upgraded.
If you play a pirated copy of Fossil Fighters: Champions, buying the Fossil Filter will cause you to only dig up Normal Rocks. 
In Fossil Fighters: Frontier, the Fossil Sonar no longer has individual components - instead, there are ten sonars. The basic Fossil Sonar is available once the player gets a Bone Buggy, and the four other normal sonars can be purchased in the Garage. Each upgraded version of the basic sonar allows the player to discover new fossils. EX versions of each level of the sonar can be won by completing the 1★-5★ tournaments of the Seven Scramble Barnum Cup. The EX Fossil Sonars display data of fossils that haven't been excavated yet - players can check what element a fossil is, what Vivosaur it belongs to, and what part it is. Players can switch sonars in the Garage.
Unlike in the DS games, the Frontier Fossil Sonar displays data on fossils before the player cleans them. Nearby fossils are automatically displayed on the area map on the lower screen and in the Dig Site itself on the top screen as triangular icons. When the player is close enough to them, they will become dinosaur skulls on the lower screen, and if an EX Fossil Sonar is equipped, the skulls will be colored to match the element of the fossil. Triggering the sonar with the L button when near one of the icons focuses the screen on the location of the fossil and brings up a box with information about it. The player can use the D-pad to switch between multiple fossils if there is more than one in the range of the sonar.
Frontier also introduces Challenge Routes, which players can complete to earn rare fossils. Different levels of the Sonar are required to find different fossils.