A group of supporters from the Bavarian outfit were seen - and heard - abusing the club's new signing during Bayern's 15-0 friendly victory over a Trentino selection side.
Neuer joined Bayern for £16.16 million from rival Schalke last month but his arrival at the Allianz Arena has angered a section of the club's die-hard fans.
Neuer played 45 minutes before being replaced by Hans-Jorg Butt in the friendly at half-time and was jeered off the pitch with fans holding up banners directed at the 25-year-old.
One such banner reportedly read: "You may catch as many balls as you like, but we will never accept you in this shirt."
Evidently, Bayern fans have not forgiven the former Schalke keeper for mocking their club legend Oliver Kahn by mimicking his title celebrations two years ago.