diff --git a/poetry.lock b/poetry.lock
index 2fb215fe..7e71f6cb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -3131,4 +3131,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.7,<3.12"
-content-hash = "211348130ff5674b03a24fe52822c7985ffa25bafe62ea7579eb17224b718b25"
+content-hash = "a357c428fa8c73c70766bfe27c52d6ea53713a3f71dc83134a61fc2180a6104e"
diff --git a/pyproject.toml b/pyproject.toml
index 19e1f9b5..320ee8b5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -52,6 +52,7 @@ boutiques = "^0.5.25"
 more-itertools = ">=8,<10"
 cached-property = "^1.5.2"
 pvandyken-deprecated = "0.0.3"
+importlib_metadata = [ { version = "^6.6.0", python = "<3.8" } ]
 
 #  Below are non-direct dependencies (i.e. dependencies of other depenencies)
 #  specified to ensure a version with a pre-built wheel is installed depending
diff --git a/snakebids/app.py b/snakebids/app.py
index 518c73e0..c9d9ac1b 100644
--- a/snakebids/app.py
+++ b/snakebids/app.py
@@ -13,6 +13,11 @@
 import snakemake
 from snakemake.io import load_configfile
 
+if sys.version_info >= (3, 8):
+    from importlib import metadata
+else:
+    import importlib_metadata as metadata
+
 from snakebids.cli import (
     SnakebidsArgs,
     add_dynamic_args,
@@ -207,7 +212,12 @@ def run_snakemake(self) -> None:
         # Write the config file
         write_config_file(
             config_file=new_config_file,
-            data=app.config,
+            data=dict(
+                app.config,
+                snakemake_version=metadata.version("snakemake"),
+                snakebids_version=metadata.version("snakebids"),
+                app_version=app.get_app_version() or "unknown",
+            ),
             force_overwrite=True,
         )
 
@@ -240,6 +250,13 @@ def create_descriptor(self, out_file: PathLike[str] | str) -> None:
         )
         new_descriptor.save(out_file)  # type: ignore
 
+    def get_app_version(self) -> str | None:
+        """Attempt to get the app version, returning None if we can't."""
+        try:
+            return metadata.version(self.snakemake_dir.name)
+        except metadata.PackageNotFoundError:
+            return None
+
 
 def update_config(config: dict[str, Any], snakebids_args: SnakebidsArgs) -> None:
     """Add snakebids arguments to config in-place."""