I am currently using QIIME 2 on an Apple Silicon Mac (MacBook Pro with an M2 chip), and my current QIIME 2 environment is running through Rosetta using the osx-64 architecture.
I recently noticed that Apple has announced an important change regarding Rosetta.
According to Apple's official documentation, Rosetta will be available on Apple Silicon Macs running macOS 27 and earlier, while starting with macOS 28, Rosetta functionality will be limited to certain older, unmaintained games that depend on Intel-based frameworks. This appears to mean that general Intel/x86_64 applications and components will no longer be supported through Rosetta on macOS 28.
Apple's documentation:
This raises a concern for users who currently run QIIME 2 on Apple Silicon Macs using the osx-64 environment under Rosetta.
My current environment is:
Mac: MacBook Pro, Apple M2
OS: macOS 27
QIIME 2: 2025.10
Conda platform: osx-64
Python: x86_64
R within the QIIME 2 environment: x86_64
Rosetta: currently required
I have confirmed that the actual QIIME 2 Python executable and the R executable inside the environment are both x86_64 binaries.
I also noticed the QIIME 2 announcement that separate osx-64 and arm-64 environment files were being introduced starting around the 2026.4 development cycle.
Given this transition, I would appreciate clarification on the following points:
Is the current arm-64 QIIME 2 environment intended to become the supported native Apple Silicon solution going forward?
For Apple Silicon users, should we expect the current arm-64 distribution to be fully usable without Rosetta for the standard QIIME 2 amplicon workflow?
Are there any important QIIME 2 plugins or dependencies that are currently still restricted to osx-64 and therefore may prevent a completely native ARM64 installation?
For users currently running QIIME 2 through osx-64 + Rosetta, what is the recommended migration strategy before upgrading to macOS 28?
For example:
migrate to the new arm-64 environment,
remain on macOS 27,
or use a Linux/container-based environment.
How stable/mature is the arm-64 distribution at this point for research workflows?
In particular, should users expect the same plugin availability and functionality as the osx-64 distribution?
Is there a planned timeline for fully deprecating osx-64 support on macOS, and will the QIIME 2 team provide migration guidance for existing Apple Silicon users before macOS 28?
I am asking because I would like to prepare my analysis environment before upgrading to macOS 28 rather than discovering compatibility problems after the upgrade.
Any guidance on the expected QIIME 2 support path for Apple Silicon users would be greatly appreciated.
Thanks for reaching out, these are some really great (and timely) questions!
This deprecation timeline has been on our radar this year, in addition to another osx-64 related deadline in fall of 2027. We currently build all of our environment files using Github's osx-64 and linux-64 runners; in August of 2027, the last remaining osx-64 runner will be fully deprecated, leaving us with arm64 as the only available osx runners after that point in time.
Because of this upcoming deprecation, we have started building/attempting to build on arm64 for our osx-supported distributions: tiny & qiime2 (formerly amplicon). As of 2026.4, we have osx-arm64 builds for the tiny distribution (as you already mentioned); we have been attempting to build arm64 for qiime2 as well, but there are still some remaining dependencies that don't yet have arm64 builds available on conda.
Our current plan after the 2026.10 release is to create a parallel 'qiime2-arm64' distribution that mirrors the current qiime2 distribution as closely as possible, but removes the blocking dependencies that don't yet have arm builds available on conda. We are still determining the minimal list of blockers for this, so I don't have a specific answer yet as to what this 'mirrored' distribution will look like immediately - but the overall goal here is to have this available for use by the 2027.1 release, and to have it in its final state by the 2027.4 release.
What this will look like as a user is that you'll be able to natively install the tiny and/or qiime2 distributions on osx-arm64; we will also retain all of our historical osx-64 builds, and will continue to build tiny and qiime2 on osx-64 (in addition to the new arm builds) up until the runner deprecation. This means that anyone who still has an intel mac can use the available environment files up through our July 2027 release, the last supported release on the osx-64 runners.
For the moshpit and pathogenome distributions, these will remain as they are now - just supported on linux-64, so the recommendations there won't change.
Hopefully this helps address your current concerns; please let me know if you have any further questions on this! We will make sure to provide updates on the forum and in our upcoming releases regarding these changes so that there aren't any unexpected surprises before next fall.
This clarifies the situation and the timeline very well. It is reassuring to know that the QIIME 2 team is already working toward an osx-arm64 distribution and that the transition is being planned well ahead of the osx-64 runner deprecation.
The timeline for the parallel qiime2-arm64 distribution and the continued availability of osx-64 builds through the July 2027 release is especially helpful for planning the transition on Apple Silicon Macs.
Thank you again for the detailed response and for keeping the community informed!
