Do you use the embedded terminal widget at the bottom to execute the command (this is setting "execute programs in the VTE" in the preferences dialog in the VTE tab)? Or is there a new terminal window popping out to execute the command?
In the former case, what does `echo $PATH` show and how does it look like when you check the `$PATH` in a normal terminal where it works?
In the latter case, play with the setting "Terminal" in the "Tools" tab in the preferences dialog (https://geany.org/manual/#tools-preferences). You could try another terminal emulator or change the command to force it executing a Bash. It could be that another shell is started in the terminal emulator and so your `.bashrc` is not used.
It seems you posted this also on https://askubuntu.com/questions/1540536/geany-terminal-path, linking the issues could help others to not double the work trying to help you.