The 20-year-old joined the Hornets last month after his contract with Scottish Premiership champions Rangers expired.
Mebude did not make a senior appearance for Rangers, but he scored two goals in 11 league outings during a loan spell at Queen of the South last season.
Premier League Watford have the option to recall Mebude from his loan spell with the Dons in January.
The Scotland Under-19 international becomes Wimbledon's eighth signing of the summer transfer window.
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