From Guide for Organic Livestock Producers.pdf @ www.ams.usda.gov/nop I will make a case for yes, microchipped animals are organic but then again I am not affiliated with USDA so you might want to check with them.
CHAPTER 18 PHYSICAL ALTERATIONS
The term “physical alterations” refers to irreversible procedures that alter the natural appearance or function of animals. They are typically used for five reasons in live-stock management:
- For identification (e.g., branding, tattooing, ear tags, and ear notching)
- To prevent injury from fighting or cannibalism among animals (e.g., beak trimming, dehorning, tail clipping, and castration)
- To prevent damage to pastures (e.g., noserings in hogs)
- To improve product quality and marketability (e.g., castration and caponization)
- For livestock health (e.g., tail docking in sheep)
According to the USDA organic regulations, physical alterations are permitted “as needed to promote the animal’s welfare” as well as to maintain individual identification of mammals. Convenience for the producer should not be construed as “animal welfare.”
[..]
A further requirement of the USDA organic regulations is that physical alterations be done “in a manner that minimizes pain and stress.” For example, it is desirable to castrate male calves at a very young age, as opposed to later in life when the pain and stress is much greater. Another example is freeze branding, which uses dry ice and is considered more humane than fire branding using electrically or fire-heated metal.
So obviously "physical alterations" to maintain individual identification of mammals - which is what I suppose microchipping is for - is permitted. Even more so if done “in a manner that minimizes pain and stress.” While I would have guessed that microchipping is less painful than branding some sources claim them to be on a par. So providing the same level of discomfort would suggest it to be fine.
Again, it seems to be prudent to check with the respective authorities not only whether microchipping is permitted in organic operations but if it is recognised as an approved system of identification at all.