diff --git a/packages/opencode/src/session/compaction.ts b/packages/opencode/src/session/compaction.ts
index 9245426057c1..c2513a1dea62 100644
--- a/packages/opencode/src/session/compaction.ts
+++ b/packages/opencode/src/session/compaction.ts
@@ -105,6 +105,7 @@ export namespace SessionCompaction {
     abort: AbortSignal
     auto: boolean
   }) {
+    const session = await Session.get(input.sessionID)
     const userMessage = input.messages.findLast((m) => m.info.id === input.parentID)!.info as MessageV2.User
     const agent = await Agent.get("compaction")
     const model = agent.model
@@ -120,7 +121,7 @@ export namespace SessionCompaction {
       variant: userMessage.variant,
       summary: true,
       path: {
-        cwd: Instance.directory,
+        cwd: session.directory,
         root: Instance.worktree,
       },
       cost: 0,
diff --git a/packages/opencode/src/session/prompt.ts b/packages/opencode/src/session/prompt.ts
index 7b20cd1d8576..d0083e890726 100644
--- a/packages/opencode/src/session/prompt.ts
+++ b/packages/opencode/src/session/prompt.ts
@@ -385,7 +385,7 @@ export namespace SessionPrompt {
           agent: task.agent,
           variant: lastUser.variant,
           path: {
-            cwd: Instance.directory,
+            cwd: session.directory,
             root: Instance.worktree,
           },
           cost: 0,
@@ -610,7 +610,7 @@ export namespace SessionPrompt {
           agent: agent.name,
           variant: lastUser.variant,
           path: {
-            cwd: Instance.directory,
+            cwd: session.directory,
             root: Instance.worktree,
           },
           cost: 0,
@@ -1572,7 +1572,7 @@ NOTE: At any point in time through this workflow you should feel free to ask the
       agent: input.agent,
       cost: 0,
       path: {
-        cwd: Instance.directory,
+        cwd: session.directory,
         root: Instance.worktree,
       },
       time: {
@@ -1662,7 +1662,7 @@ NOTE: At any point in time through this workflow you should feel free to ask the
     const matchingInvocation = invocations[shellName] ?? invocations[""]
     const args = matchingInvocation?.args
 
-    const cwd = Instance.directory
+    const cwd = session.directory
     const shellEnv = await Plugin.trigger("shell.env", { cwd }, { env: {} })
     const proc = spawn(shell, args, {
       cwd,
diff --git a/packages/opencode/test/session/worktree-directory.test.ts b/packages/opencode/test/session/worktree-directory.test.ts
new file mode 100644
index 000000000000..cedbeacefaf4
--- /dev/null
+++ b/packages/opencode/test/session/worktree-directory.test.ts
@@ -0,0 +1,261 @@
+import { describe, test, expect } from "bun:test"
+import { Instance } from "../../src/project/instance"
+import { Session } from "../../src/session"
+import { MessageV2 } from "../../src/session/message-v2"
+import { Identifier } from "../../src/id/id"
+import { tmpdir } from "../fixture/fixture"
+
+describe("session worktree directory in messages", () => {
+  test("messages should use session.directory not Instance.directory", async () => {
+    await using tmp = await tmpdir({ git: true })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        // Create a session with a specific directory (simulating worktree)
+        const session = await Session.create({})
+
+        // Verify we use session.directory, not Instance.directory
+        const expectedCwd = session.directory
+        const expectedRoot = Instance.worktree
+
+        // Create a user message
+        const userMessage: MessageV2.User = {
+          id: Identifier.ascending("message"),
+          sessionID: session.id,
+          time: { created: Date.now() },
+          role: "user",
+          agent: "general",
+          model: {
+            providerID: "test",
+            modelID: "test-model",
+          },
+        }
+        await Session.updateMessage(userMessage)
+
+        const userPart: MessageV2.Part = {
+          type: "text",
+          id: Identifier.ascending("part"),
+          messageID: userMessage.id,
+          sessionID: session.id,
+          text: "test message",
+        }
+        await Session.updatePart(userPart)
+
+        // Verify that when creating assistant messages, we use session.directory
+        // This simulates what prompt.ts should do (and what the fix addresses)
+        const assistantMessage: MessageV2.Assistant = {
+          id: Identifier.ascending("message"),
+          sessionID: session.id,
+          parentID: userMessage.id,
+          role: "assistant",
+          mode: "general",
+          agent: "general",
+          variant: undefined,
+          cost: 0,
+          tokens: {
+            input: 0,
+            output: 0,
+            reasoning: 0,
+            cache: { read: 0, write: 0 },
+          },
+          modelID: "test-model",
+          providerID: "test",
+          time: { created: Date.now() },
+          path: {
+            cwd: expectedCwd, // FIXED: should be session.directory, not Instance.directory
+            root: expectedRoot,
+          },
+        }
+        await Session.updateMessage(assistantMessage)
+
+        // Fetch the message back from the database (stream is an async generator)
+        const messages = []
+        for await (const msg of MessageV2.stream(session.id)) {
+          messages.push(msg)
+        }
+        const createdAssistant = messages.find((m: MessageV2.WithParts) => m.info.id === assistantMessage.id)
+
+        // Verify the directory is correct - it should match session.directory
+        expect((createdAssistant.info as MessageV2.Assistant)?.path.cwd).toBe(expectedCwd)
+        expect((createdAssistant.info as MessageV2.Assistant)?.path.root).toBe(expectedRoot)
+      },
+    })
+  })
+
+  test("subtask messages should use session.directory", async () => {
+    await using tmp = await tmpdir({ git: true })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const session = await Session.create({})
+
+        // Verify session directory
+        const expectedCwd = session.directory
+        const expectedRoot = Instance.worktree
+
+        // Create a user message
+        const userMessage: MessageV2.User = {
+          id: Identifier.ascending("message"),
+          sessionID: session.id,
+          time: { created: Date.now() },
+          role: "user",
+          agent: "general",
+          model: {
+            providerID: "test",
+            modelID: "test-model",
+          },
+        }
+        await Session.updateMessage(userMessage)
+
+        const userPart: MessageV2.Part = {
+          type: "text",
+          id: Identifier.ascending("part"),
+          messageID: userMessage.id,
+          sessionID: session.id,
+          text: "run subtask",
+        }
+        await Session.updatePart(userPart)
+
+        // Create assistant message for subtask
+        const assistantMessage: MessageV2.Assistant = {
+          id: Identifier.ascending("message"),
+          sessionID: session.id,
+          parentID: userMessage.id,
+          role: "assistant",
+          mode: "general",
+          agent: "general",
+          variant: undefined,
+          cost: 0,
+          tokens: {
+            input: 0,
+            output: 0,
+            reasoning: 0,
+            cache: { read: 0, write: 0 },
+          },
+          modelID: "test-model",
+          providerID: "test",
+          time: { created: Date.now() },
+          path: {
+            cwd: expectedCwd,
+            root: expectedRoot,
+          },
+        }
+        await Session.updateMessage(assistantMessage)
+
+        // Fetch the message back
+        const messages = []
+        for await (const msg of MessageV2.stream(session.id)) {
+          messages.push(msg)
+        }
+        const createdAssistant = messages.find((m: MessageV2.WithParts) => m.info.id === assistantMessage.id)
+
+        // Verify the directory is session.directory, not Instance.directory
+        expect((createdAssistant.info as MessageV2.Assistant)?.path.cwd).toBe(expectedCwd)
+        expect((createdAssistant.info as MessageV2.Assistant)?.path.root).toBe(expectedRoot)
+      },
+    })
+  })
+
+  test("compaction messages should use session.directory", async () => {
+    await using tmp = await tmpdir({ git: true })
+
+    await Instance.provide({
+      directory: tmp.path,
+      fn: async () => {
+        const session = await Session.create({})
+
+        const expectedCwd = session.directory
+        const expectedRoot = Instance.worktree
+
+        // Create user and assistant messages
+        const userMessage: MessageV2.User = {
+          id: Identifier.ascending("message"),
+          sessionID: session.id,
+          time: { created: Date.now() },
+          role: "user",
+          agent: "general",
+          model: {
+            providerID: "test",
+            modelID: "test-model",
+          },
+        }
+        await Session.updateMessage(userMessage)
+
+        const userPart: MessageV2.Part = {
+          type: "text",
+          id: Identifier.ascending("part"),
+          messageID: userMessage.id,
+          sessionID: session.id,
+          text: "original message",
+        }
+        await Session.updatePart(userPart)
+
+        // Create assistant message
+        const assistantMessage: MessageV2.Assistant = {
+          id: Identifier.ascending("message"),
+          sessionID: session.id,
+          parentID: userMessage.id,
+          role: "assistant",
+          mode: "general",
+          agent: "general",
+          variant: undefined,
+          cost: 0,
+          tokens: {
+            input: 0,
+            output: 0,
+            reasoning: 0,
+            cache: { read: 0, write: 0 },
+          },
+          modelID: "test-model",
+          providerID: "test",
+          time: { created: Date.now() },
+          path: {
+            cwd: expectedCwd,
+            root: expectedRoot,
+          },
+        }
+        await Session.updateMessage(assistantMessage)
+
+        // Create a compaction message (simulating compaction.ts)
+        const compactionMessage: MessageV2.Assistant = {
+          id: Identifier.ascending("message"),
+          sessionID: session.id,
+          parentID: assistantMessage.id,
+          role: "assistant",
+          mode: "compaction",
+          agent: "compaction",
+          variant: undefined,
+          summary: true,
+          cost: 0,
+          tokens: {
+            input: 0,
+            output: 0,
+            reasoning: 0,
+            cache: { read: 0, write: 0 },
+          },
+          modelID: "test-model",
+          providerID: "test",
+          time: { created: Date.now() },
+          path: {
+            cwd: expectedCwd,
+            root: expectedRoot,
+          },
+        }
+        await Session.updateMessage(compactionMessage)
+
+        // Fetch the message back
+        const messages = []
+        for await (const msg of MessageV2.stream(session.id)) {
+          messages.push(msg)
+        }
+        const createdCompaction = messages.find((m: MessageV2.WithParts) => m.info.id === compactionMessage.id)
+
+        // Verify the directory is session.directory, not Instance.directory
+        expect((createdCompaction.info as MessageV2.Assistant)?.path.cwd).toBe(expectedCwd)
+        expect((createdCompaction.info as MessageV2.Assistant)?.path.root).toBe(expectedRoot)
+      },
+    })
+  })
+})
\ No newline at end of file