diff --git a/crates/pile-config/src/lib.rs b/crates/pile-config/src/lib.rs
index 76ef44f..678de58 100644
--- a/crates/pile-config/src/lib.rs
+++ b/crates/pile-config/src/lib.rs
@@ -51,6 +51,10 @@ pub struct S3Credentials {
 pub enum Source {
 	/// A directory of files
 	Filesystem {
+		/// If false, ignore this dataset
+		#[serde(default = "default_true")]
+		enabled: bool,
+
 		/// The directories to scan.
 		/// Must be relative.
 		path: PathBuf,
@@ -66,6 +70,10 @@ pub enum Source {
 
 	/// An S3-compatible object store bucket
 	S3 {
+		/// If false, ignore this dataset
+		#[serde(default = "default_true")]
+		enabled: bool,
+
 		bucket: String,
 		prefix: Option<String>,
 
diff --git a/crates/pile-dataset/src/dataset.rs b/crates/pile-dataset/src/dataset.rs
index c3fc64d..240232e 100644
--- a/crates/pile-dataset/src/dataset.rs
+++ b/crates/pile-dataset/src/dataset.rs
@@ -114,7 +114,15 @@ impl Datasets {
 		let mut sources = HashMap::new();
 		for (label, source) in &config.dataset.source {
 			match source {
-				Source::Filesystem { path, sidecars } => {
+				Source::Filesystem {
+					enabled,
+					path,
+					sidecars,
+				} => {
+					if !enabled {
+						continue;
+					}
+
 					sources.insert(
 						label.clone(),
 						Dataset::Dir(Arc::new(DirDataSource::new(
@@ -126,6 +134,7 @@ impl Datasets {
 				}
 
 				Source::S3 {
+					enabled,
 					bucket,
 					prefix,
 					endpoint,
@@ -133,6 +142,10 @@ impl Datasets {
 					credentials,
 					sidecars,
 				} => {
+					if !enabled {
+						continue;
+					}
+
 					match S3DataSource::new(
 						label,
 						bucket.clone(),
diff --git a/crates/pile-value/src/source/s3.rs b/crates/pile-value/src/source/s3.rs
index e635580..b4eaf55 100644
--- a/crates/pile-value/src/source/s3.rs
+++ b/crates/pile-value/src/source/s3.rs
@@ -92,10 +92,15 @@ impl S3DataSource {
 
 	async fn make_item(self: &Arc<Self>, key: impl Into<SmartString<LazyCompact>>) -> Item {
 		let key: SmartString<LazyCompact> = key.into();
-		let mime = mime_guess::from_path(key.as_str()).first_or_octet_stream();
+		let object_path = match &self.prefix {
+			Some(x) => format!("{x}/{key}").into(),
+			None => key.clone(),
+		};
+
+		let mime = mime_guess::from_path(object_path.as_str()).first_or_octet_stream();
 
 		let sidecar = if self.sidecars {
-			self.find_sidecar_key(key.as_str())
+			self.find_sidecar_key(object_path.as_str())
 				.await
 				.map(|sidecar_key| {
 					Box::new(Item::S3 {
@@ -124,11 +129,17 @@ impl DataSource for Arc<S3DataSource> {
 			return Ok(None);
 		}
 
+		let key: SmartString<LazyCompact> = key.into();
+		let key = match &self.prefix {
+			Some(x) => format!("{x}/{key}").into(),
+			None => key,
+		};
+
 		let result = self
 			.client
 			.head_object()
 			.bucket(self.bucket.as_str())
-			.key(key)
+			.key(key.as_str())
 			.send()
 			.await;
 
diff --git a/crates/pile/src/command/annotate.rs b/crates/pile/src/command/annotate.rs
index 90912b3..4a5434d 100644
--- a/crates/pile/src/command/annotate.rs
+++ b/crates/pile/src/command/annotate.rs
@@ -58,7 +58,7 @@ impl CliCmd for AnnotateCommand {
 
 		for (name, source) in &ds.config.dataset.source {
 			match source {
-				Source::Filesystem { path, sidecars } => {
+				Source::Filesystem { path, sidecars, .. } => {
 					if !sidecars {
 						warn!("Source {name} does not have sidecars enabled, skipping");
 						continue;