The 17-year-old Peckham rider qualified through the time trials on Saturday with a time of 27.855 to reach the racing the following day.
The Motos took on a best of three format with the top four of six winning through to the next round and in a heat featuring Kristens Krigers, who went on to make the final, it was always going to be a tough ask for Isidore to qualify, especially given he was just returning after a month out injured.
A fifth-place finish saw him just miss out on qualification but competing in the Junior Elite category ensured the Sky Academy Sports Scholar was able to test himself at a World Championships again after a year plagued by injuries.
Isidore made it clear beforehand that he was travelling to Rotterdam solely for the experience and having got that he can now focus on a return to form and full fitness with the prospect of a place at the GB BMX Academy in Manchester another key motivation.
Dutch rider Niek Kiemann took the Junior Elite crown with Australia's Sam Willoughby winning the Men's Elite title. Tre White took the bronze for Great Britain.