diff --git a/CHANGES.md b/CHANGES.md
index b899f35f..f021d562 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -58,6 +58,11 @@ our broader "workflows as programs" endeavor.
   that work is being done when checks take a second or two.
   ([#418](https://github.com/nextstrain/cli/pull/418))
 
+* The Conda runtime now uses Micromamba 2.1.0 (upgraded from 1.5.8) to manage
+  the runtime environment. The newer version fixes the installation error for
+  packages that include the `_x86_64-microarch-level` virtual package dependency.
+  ([#430](https://github.com/nextstrain/cli/pull/430))
+
 
 # 9.0.0 (24 March 2025)
 
diff --git a/nextstrain/cli/runner/conda.py b/nextstrain/cli/runner/conda.py
index bfb9db1a..0e119fe2 100644
--- a/nextstrain/cli/runner/conda.py
+++ b/nextstrain/cli/runner/conda.py
@@ -67,7 +67,7 @@
     <https://anaconda.org/conda-forge/micromamba/>`__, or the special string
     ``latest``.
 
-    Defaults to ``1.5.8``.
+    Defaults to ``2.1.0``.
 """
 
 import json
@@ -100,7 +100,7 @@
 
 # If you update the version pin below, please update the docstring above too.
 MICROMAMBA_VERSION = os.environ.get("NEXTSTRAIN_CONDA_MICROMAMBA_VERSION") \
-                  or "1.5.8"
+                  or "2.1.0"
 
 NEXTSTRAIN_CHANNEL = os.environ.get("NEXTSTRAIN_CONDA_CHANNEL") \
                   or "nextstrain"