diff --git a/app/gitspace/orchestrator/container/container_orchestrator.go b/app/gitspace/orchestrator/container/container_orchestrator.go
index e11267a86..ad7df5885 100644
--- a/app/gitspace/orchestrator/container/container_orchestrator.go
+++ b/app/gitspace/orchestrator/container/container_orchestrator.go
@@ -29,6 +29,7 @@ type Orchestrator interface {
 		gitspaceConfig *types.GitspaceConfig,
 		devcontainerConfig *types.DevcontainerConfig,
 		infra *infraprovider.Infrastructure,
+		repoName string,
 	) (*StartResponse, error)
 
 	// StopGitspace stops and removes the gitspace container.
diff --git a/app/gitspace/orchestrator/container/embedded_docker.go b/app/gitspace/orchestrator/container/embedded_docker.go
index 8bf5e967f..f671b5adf 100644
--- a/app/gitspace/orchestrator/container/embedded_docker.go
+++ b/app/gitspace/orchestrator/container/embedded_docker.go
@@ -18,7 +18,6 @@ import (
 	"context"
 	"fmt"
 	"io"
-	"strings"
 
 	"github.com/harness/gitness/app/gitspace/logutil"
 	"github.com/harness/gitness/infraprovider"
@@ -49,8 +48,6 @@ const (
 
 type Config struct {
 	DefaultBaseImage string
-	WorkingDirectory string
-	RootSource       string
 }
 
 type EmbeddedDockerOrchestrator struct {
@@ -87,6 +84,7 @@ func (e *EmbeddedDockerOrchestrator) StartGitspace(
 	gitspaceConfig *types.GitspaceConfig,
 	devcontainerConfig *types.DevcontainerConfig,
 	infra *infraprovider.Infrastructure,
+	repoName string,
 ) (*StartResponse, error) {
 	containerName := getGitspaceContainerName(gitspaceConfig)
 
@@ -148,7 +146,7 @@ func (e *EmbeddedDockerOrchestrator) StartGitspace(
 				log.Warn().Err(loggerErr).Msgf("failed to flush log stream for gitspace ID %d", gitspaceConfig.ID)
 			}
 		}()
-
+		workingDirectory := "/" + repoName
 		startErr = e.startGitspace(
 			ctx,
 			gitspaceConfig,
@@ -158,6 +156,7 @@ func (e *EmbeddedDockerOrchestrator) StartGitspace(
 			ideService,
 			logStreamInstance,
 			infra.Storage,
+			workingDirectory,
 		)
 		if startErr != nil {
 			return nil, fmt.Errorf("failed to start gitspace %s: %w", containerName, startErr)
@@ -178,10 +177,9 @@ func (e *EmbeddedDockerOrchestrator) StartGitspace(
 	}
 
 	return &StartResponse{
-		ContainerID:      containerID,
-		ContainerName:    containerName,
-		WorkingDirectory: strings.TrimPrefix(e.config.WorkingDirectory, "/"),
-		PortsUsed:        usedPorts,
+		ContainerID:   containerID,
+		ContainerName: containerName,
+		PortsUsed:     usedPorts,
 	}, nil
 }
 
@@ -194,6 +192,7 @@ func (e *EmbeddedDockerOrchestrator) startGitspace(
 	ideService IDE,
 	logStreamInstance *logutil.LogStreamInstance,
 	volumeName string,
+	workingDirectory string,
 ) error {
 	var imageName = devcontainerConfig.Image
 	if imageName == "" {
@@ -213,6 +212,7 @@ func (e *EmbeddedDockerOrchestrator) startGitspace(
 		ideService,
 		logStreamInstance,
 		volumeName,
+		workingDirectory,
 	)
 	if err != nil {
 		return err
@@ -221,12 +221,7 @@ func (e *EmbeddedDockerOrchestrator) startGitspace(
 	var devcontainer = &Devcontainer{
 		ContainerName: containerName,
 		DockerClient:  dockerClient,
-		WorkingDir:    e.config.WorkingDirectory,
-	}
-
-	err = e.executePostCreateCommand(ctx, devcontainerConfig, devcontainer, logStreamInstance)
-	if err != nil {
-		return err
+		WorkingDir:    workingDirectory,
 	}
 
 	err = e.cloneCode(ctx, gitspaceConfig, devcontainerConfig, devcontainer, logStreamInstance)
@@ -239,6 +234,11 @@ func (e *EmbeddedDockerOrchestrator) startGitspace(
 		return err
 	}
 
+	err = e.executePostCreateCommand(ctx, devcontainerConfig, devcontainer, logStreamInstance)
+	if err != nil {
+		return err
+	}
+
 	return nil
 }
 
@@ -425,6 +425,7 @@ func (e *EmbeddedDockerOrchestrator) createContainer(
 	ideService IDE,
 	logStreamInstance *logutil.LogStreamInstance,
 	volumeName string,
+	workingDirectory string,
 ) error {
 	portUsedByIDE := ideService.PortAndProtocol()
 
@@ -466,7 +467,7 @@ func (e *EmbeddedDockerOrchestrator) createContainer(
 			{
 				Type:   mount.TypeVolume,
 				Source: volumeName,
-				Target: e.config.WorkingDirectory,
+				Target: workingDirectory,
 			},
 		},
 	}, nil, containerName)
diff --git a/app/gitspace/orchestrator/container/template/clone_git.sh b/app/gitspace/orchestrator/container/template/clone_git.sh
index cd43c5cb7..4f046e722 100644
--- a/app/gitspace/orchestrator/container/template/clone_git.sh
+++ b/app/gitspace/orchestrator/container/template/clone_git.sh
@@ -23,7 +23,7 @@ fi
 # Clone the repository only if it doesn't exist
 if [ ! -d "$repo_name" ]; then
     echo "Cloning the repository..."
-    git clone "$repo_url" --branch "$branch"
+    git clone "$repo_url" --branch "$branch" .
 else
     echo "Repository already exists. Skipping clone."
 fi
diff --git a/app/gitspace/orchestrator/orchestrator_impl.go b/app/gitspace/orchestrator/orchestrator_impl.go
index 7722d287d..83158668f 100644
--- a/app/gitspace/orchestrator/orchestrator_impl.go
+++ b/app/gitspace/orchestrator/orchestrator_impl.go
@@ -113,7 +113,7 @@ func (o orchestrator) StartGitspace(
 
 	o.emitGitspaceEvent(ctx, gitspaceConfig, enum.GitspaceEventTypeAgentGitspaceCreationStart)
 
-	startResponse, err := o.containerOrchestrator.StartGitspace(ctx, gitspaceConfig, devcontainerConfig, infra)
+	startResponse, err := o.containerOrchestrator.StartGitspace(ctx, gitspaceConfig, devcontainerConfig, infra, repoName)
 	if err != nil {
 		o.emitGitspaceEvent(ctx, gitspaceConfig, enum.GitspaceEventTypeAgentGitspaceCreationFailed)
 
@@ -130,7 +130,7 @@ func (o orchestrator) StartGitspace(
 		ideURL = url.URL{
 			Scheme:   "http",
 			Host:     infra.Host + ":" + port,
-			RawQuery: filepath.Join("folder=", startResponse.WorkingDirectory, repoName),
+			RawQuery: filepath.Join("folder=", repoName),
 		}
 	} else if gitspaceConfig.IDE == enum.IDETypeVSCode {
 		// TODO: the following userID is hard coded and should be changed.
@@ -142,7 +142,7 @@ func (o orchestrator) StartGitspace(
 				"ssh-remote+%s@%s:%s",
 				userID,
 				infra.Host,
-				filepath.Join(port, startResponse.WorkingDirectory, repoName),
+				filepath.Join(port, repoName),
 			),
 		}
 	}
diff --git a/cli/operations/server/config.go b/cli/operations/server/config.go
index efcf958f6..e4f8cb325 100644
--- a/cli/operations/server/config.go
+++ b/cli/operations/server/config.go
@@ -408,7 +408,6 @@ func ProvideIDEVSCodeWebConfig(config *types.Config) *container.VSCodeWebConfig
 func ProvideGitspaceContainerOrchestratorConfig(config *types.Config) *container.Config {
 	return &container.Config{
 		DefaultBaseImage: config.Gitspace.DefaultBaseImage,
-		WorkingDirectory: config.Gitspace.WorkingDirectory,
 	}
 }
 
diff --git a/types/config.go b/types/config.go
index dd7125abc..527c6c4b8 100644
--- a/types/config.go
+++ b/types/config.go
@@ -401,9 +401,6 @@ type Config struct {
 		// DefaultBaseImage is used to create the Gitspace when no devcontainer.json is absent or doesn't have image.
 		DefaultBaseImage string `envconfig:"GITNESS_GITSPACE_DEFAULT_BASE_IMAGE" default:"mcr.microsoft.com/devcontainers/base:dev-ubuntu-24.04"` //nolint:lll
 
-		// WorkingDirectory is the default working directory in the Gitspace container.
-		WorkingDirectory string `envconfig:"GITNESS_GITSPACE_WORKING_DIR" default:"/gitspace"`
-
 		Enable bool `envconfig:"GITNESS_GITSPACE_ENABLE" default:"false"`
 
 		Events struct {