diff --git a/e2e/tasks/test_task_source_freshness_with_cwd b/e2e/tasks/test_task_source_freshness_with_cwd
new file mode 100644
index 0000000000..61d3c359c3
--- /dev/null
+++ b/e2e/tasks/test_task_source_freshness_with_cwd
@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+
+cat <<EOF >mise.toml
+[tasks.cwd_task]
+run = "cat input.txt"
+dir = "{{cwd}}"
+sources = ["input.txt"]
+outputs = { auto = true }
+EOF
+
+mkdir a
+mkdir b
+
+echo "running a" >a/input.txt
+echo "running b 1" >b/input.txt
+
+# Should first run and then skip
+pushd a
+assert "mise run -q cwd_task" "running a"
+assert_empty "mise run -q cwd_task"
+popd
+
+# Should first run again as directory was changed and then skip
+pushd b
+assert "mise run -q cwd_task" "running b 1"
+assert_empty "mise run -q cwd_task"
+popd
+
+echo "running b 2" >b/input.txt
+
+# Should still skip as input in this directory was not changed
+pushd a
+assert_empty "mise run -q cwd_task"
+popd
+
+# Should run again as input in this directory was changed
+pushd b
+assert "mise run -q cwd_task" "running b 2"
+assert_empty "mise run -q cwd_task"
+popd
diff --git a/src/cli/tasks/info.rs b/src/cli/tasks/info.rs
index 5051e31fad..1dd3b302ed 100644
--- a/src/cli/tasks/info.rs
+++ b/src/cli/tasks/info.rs
@@ -8,6 +8,7 @@ use crate::config::Config;
 use crate::file::display_path;
 use crate::task::Task;
 use crate::task::task_fetcher::TaskFetcher;
+use crate::task::task_source_checker::task_cwd;
 use crate::ui::info;
 
 /// Get information about a task
@@ -93,7 +94,8 @@ impl TasksInfo {
         if !task.sources.is_empty() {
             info::inline_section("Sources", task.sources.join(", "))?;
         }
-        let outputs = task.outputs.paths(task);
+        let root = task_cwd(task, config).await?;
+        let outputs = task.outputs.paths(task, &root);
         if !outputs.is_empty() {
             info::inline_section("Outputs", outputs.join(", "))?;
         }
diff --git a/src/cli/tasks/validate.rs b/src/cli/tasks/validate.rs
index 22f7529c57..faa73602a0 100644
--- a/src/cli/tasks/validate.rs
+++ b/src/cli/tasks/validate.rs
@@ -508,7 +508,7 @@ impl TasksValidate {
         let mut issues = Vec::new();
 
         // Validate output patterns if they exist
-        let paths = task.outputs.paths(task);
+        let paths = task.outputs.patterns();
         for path in paths {
             // Try to compile as glob pattern
             if let Err(e) = globset::GlobBuilder::new(&path).build() {
diff --git a/src/task/task_source_checker.rs b/src/task/task_source_checker.rs
index e6cd104106..5ca3edce39 100644
--- a/src/task/task_source_checker.rs
+++ b/src/task/task_source_checker.rs
@@ -142,11 +142,11 @@ pub async fn sources_are_fresh(task: &Task, config: &Arc<Config>) -> Result<bool
         } else {
             file_metadatas_to_hash(&source_metadatas)
         };
-        let source_hash_path = sources_hash_path(task, use_content_hash);
+        let source_hash_path = sources_hash_path(task, &root, use_content_hash);
         if let Some(dir) = source_hash_path.parent() {
             file::create_dir_all(dir)?;
         }
-        if source_existing_hash(task, use_content_hash).is_some_and(|h| h != source_hash) {
+        if source_existing_hash(task, &root, use_content_hash).is_some_and(|h| h != source_hash) {
             debug!(
                 "source {} hash mismatch in {}",
                 if use_content_hash {
@@ -160,7 +160,7 @@ pub async fn sources_are_fresh(task: &Task, config: &Arc<Config>) -> Result<bool
             return Ok(false);
         }
         let sources = get_last_modified_from_metadatas(&source_metadatas);
-        let outputs = get_last_modified(&root, &task.outputs.paths(task))?;
+        let outputs = get_last_modified(&root, &task.outputs.paths(task, &root))?;
         file::write(&source_hash_path, &source_hash)?;
         trace!("sources: {sources:?}, outputs: {outputs:?}");
         match (sources, outputs) {
@@ -186,7 +186,8 @@ pub async fn save_checksum(task: &Task, config: &Arc<Config>) -> Result<()> {
         return Ok(());
     }
     if task.outputs.is_auto() {
-        for p in task.outputs.paths(task) {
+        let root = task_cwd(task, config).await?;
+        for p in task.outputs.paths(task, &root) {
             debug!("touching auto output file: {p}");
             file::touch_file(&PathBuf::from(&p))?;
         }
@@ -194,7 +195,7 @@ pub async fn save_checksum(task: &Task, config: &Arc<Config>) -> Result<()> {
         // Check if explicitly defined outputs were generated
         // Use task_cwd to respect the task's dir setting, matching sources_are_fresh behavior
         let root = task_cwd(task, config).await?;
-        for output in task.outputs.paths(task) {
+        for output in task.outputs.paths(task, &root) {
             let output_exists = if is_glob_pattern(&output) {
                 // For glob patterns, check if any files match
                 let pattern = root.join(&output);
@@ -223,10 +224,11 @@ pub async fn save_checksum(task: &Task, config: &Arc<Config>) -> Result<()> {
 }
 
 /// Get the path to store source hashes for a task
-fn sources_hash_path(task: &Task, content_hash: bool) -> PathBuf {
+fn sources_hash_path(task: &Task, root: &Path, content_hash: bool) -> PathBuf {
     let mut hasher = DefaultHasher::new();
     task.hash(&mut hasher);
     task.config_source.hash(&mut hasher);
+    root.hash(&mut hasher);
     let hash = format!("{:x}", hasher.finish());
     let suffix = if content_hash { "-content" } else { "" };
     dirs::STATE
@@ -235,8 +237,8 @@ fn sources_hash_path(task: &Task, content_hash: bool) -> PathBuf {
 }
 
 /// Get the existing source hash for a task, if it exists
-fn source_existing_hash(task: &Task, content_hash: bool) -> Option<String> {
-    let path = sources_hash_path(task, content_hash);
+fn source_existing_hash(task: &Task, root: &Path, content_hash: bool) -> Option<String> {
+    let path = sources_hash_path(task, root, content_hash);
     if path.exists() {
         Some(file::read_to_string(&path).unwrap_or_default())
     } else {
diff --git a/src/task/task_sources.rs b/src/task/task_sources.rs
index 823d57cef6..17435472a7 100644
--- a/src/task/task_sources.rs
+++ b/src/task/task_sources.rs
@@ -3,6 +3,7 @@ use crate::task::Task;
 use serde::ser::{SerializeMap, SerializeSeq};
 use serde::{Deserialize, Deserializer, Serialize};
 use std::hash::{DefaultHasher, Hash, Hasher};
+use std::path::Path;
 
 #[derive(Debug, Clone, Eq, PartialEq, strum::EnumIs)]
 pub enum TaskOutputs {
@@ -32,17 +33,25 @@ impl TaskOutputs {
         }
     }
 
-    pub fn paths(&self, task: &Task) -> Vec<String> {
+    pub fn patterns(&self) -> Vec<String> {
         match self {
             TaskOutputs::Files(files) => files.clone(),
-            TaskOutputs::Auto => vec![self.auto_path(task)],
+            TaskOutputs::Auto => vec![],
         }
     }
 
-    fn auto_path(&self, task: &Task) -> String {
+    pub fn paths(&self, task: &Task, root: &Path) -> Vec<String> {
+        match self {
+            TaskOutputs::Files(files) => files.clone(),
+            TaskOutputs::Auto => vec![self.auto_path(task, root)],
+        }
+    }
+
+    fn auto_path(&self, task: &Task, root: &Path) -> String {
         let mut hasher = DefaultHasher::new();
         task.hash(&mut hasher);
         task.config_source.hash(&mut hasher);
+        root.hash(&mut hasher);
         let hash = format!("{:x}", hasher.finish());
         dirs::STATE
             .join("task-auto-outputs")