Nelson had won scratch gold on the opening night of the championships, leading out the pack with four laps to go and staying strong to hold off all-comers.
The Brit was straight back into action with the elimination race where home favourite Kirsten Wild was looking to make up for losing her title to Nelson the previous night.
GB add three more medals as Wild claims gold in Apeldoorn
18/10/2019 AT 17:42
The Dutch rider had been caught out at the end and finished fifth but was in no mood for mistakes this time around, keeping well out of trouble throughout.
Nelson only found herself in danger when the field was cut down to five but showed her strength when she guaranteed herself a medal, pipping Italy's Maria Confalonieri, who went out in fourth.
Poland's Nikol Plosaj had given everything for a medal, turning the last four laps into a match sprint between Wild and Nelson, with the former led out on the final circuit.
Nelson was closing around the outside but the finish line came too soon and Wild sealed her 11th European title by half a bike length, while the Brit had to be content with her team's third medal of the week.
Archibald powers GB to team pursuit gold
17/10/2019 AT 20:05
Mora Vedri wins scratch race with early break
17/10/2019 AT 18:04