In Deep Sea Zone Act 1, there is a series of buttons which require the player to backtrack through parts of the level. After pressing three specific buttons, a path will open up near the start of the level, leading to a room with an animated portrait of Cirno from the Touhou Project franchise.

In Greenflower Zone Act 1, there is a house in the upper section of the level next to a lake. If the player has all 200 Emblems, this house will have a note on it thanking the player for keeping the game alive.

This house belongs to the in-universe persona of RedXVI, an old member of the Sonic fangame community who had significant influence over Sonic Robo Blast 2's development.

The location of this note is a reference to Version 1.09 of the game, where an Easter egg was hidden on the very same house. In this version, jumping on the house would cause RedXVI to come out and send the player to an early work-in-progress version of Red Volcano Zone Act 1 if the player jumped on the house repeatedly after beating the game three times.

In the Halloween-themed unlockable level Haunted Heights Zone, one of the enemies present in the level is the Cacolantern. These enemies are a direct reference to the Cacodemons from Doom, which is notable as Sonic Robo Blast 2 is a modification of the Doom Legacy source port.