diff --git a/bundle/config/mutator/prepend_workspace_prefix.go b/bundle/config/mutator/prepend_workspace_prefix.go
index 8ba083e22..8e01dfe71 100644
--- a/bundle/config/mutator/prepend_workspace_prefix.go
+++ b/bundle/config/mutator/prepend_workspace_prefix.go
@@ -24,7 +24,6 @@ func (m *prependWorkspacePrefix) Name() string {
 var skipPrefixes = []string{
 	"/Workspace",
 	"/Volumes",
-	"/Shared",
 }
 
 func (m *prependWorkspacePrefix) Apply(ctx context.Context, b *bundle.Bundle) diag.Diagnostics {
@@ -44,12 +43,6 @@ func (m *prependWorkspacePrefix) Apply(ctx context.Context, b *bundle.Bundle) di
 					return dyn.InvalidValue, fmt.Errorf("expected string, got %s", v.Kind())
 				}
 
-				for _, prefix := range skipPrefixes {
-					if path == prefix {
-						return pv, nil
-					}
-				}
-
 				for _, prefix := range skipPrefixes {
 					if strings.HasPrefix(path, prefix) {
 						return pv, nil
diff --git a/bundle/config/mutator/prepend_workspace_prefix_test.go b/bundle/config/mutator/prepend_workspace_prefix_test.go
index 20f69fefc..287c694d3 100644
--- a/bundle/config/mutator/prepend_workspace_prefix_test.go
+++ b/bundle/config/mutator/prepend_workspace_prefix_test.go
@@ -21,7 +21,7 @@ func TestPrependWorkspacePrefix(t *testing.T) {
 		},
 		{
 			path:     "/Shared/test",
-			expected: "/Shared/test",
+			expected: "/Workspace/Shared/test",
 		},
 		{
 			path:     "/Workspace/Users/test",
diff --git a/bundle/config/validate/no_workspace_prefix_used.go b/bundle/config/validate/no_workspace_prefix_used.go
new file mode 100644
index 000000000..dd774dd1d
--- /dev/null
+++ b/bundle/config/validate/no_workspace_prefix_used.go
@@ -0,0 +1,58 @@
+package validate
+
+import (
+	"context"
+	"fmt"
+	"strings"
+
+	"github.com/databricks/cli/bundle"
+	"github.com/databricks/cli/libs/diag"
+	"github.com/databricks/cli/libs/dyn"
+)
+
+type noWorkspacePrefixUsed struct{}
+
+// NoWorkspacePrefixUsed ensures that no workspace prefix plus workspace path variable is used in the remote path.
+func NoWorkspacePrefixUsed() bundle.Mutator {
+	return &noWorkspacePrefixUsed{}
+}
+
+func (m *noWorkspacePrefixUsed) Name() string {
+	return "validate:no_workspace_prefix_used"
+}
+
+func (m *noWorkspacePrefixUsed) Apply(ctx context.Context, b *bundle.Bundle) diag.Diagnostics {
+	diags := diag.Diagnostics{}
+	prefixes := []string{
+		"/Workspace/${workspace.root_path}",
+		"/Workspace/${workspace.file_path}",
+		"/Workspace/${workspace.artifact_path}",
+		"/Workspace/${workspace.state_path}",
+	}
+
+	_, err := dyn.Walk(b.Config.Value(), func(p dyn.Path, v dyn.Value) (dyn.Value, error) {
+		vv, ok := v.AsString()
+		if !ok {
+			return v, nil
+		}
+
+		for _, prefix := range prefixes {
+			if strings.HasPrefix(vv, prefix) {
+				diags = append(diags, diag.Diagnostic{
+					Severity:  diag.Error,
+					Summary:   fmt.Sprintf("%s used in the remote path %s. Please change to use %s instead", prefix, vv, strings.ReplaceAll(vv, "/Workspace/", "")),
+					Locations: v.Locations(),
+					Paths:     []dyn.Path{p},
+				})
+			}
+		}
+
+		return v, nil
+	})
+
+	if err != nil {
+		return diag.FromErr(err)
+	}
+
+	return diags
+}
diff --git a/bundle/config/validate/no_workspace_prefix_used_test.go b/bundle/config/validate/no_workspace_prefix_used_test.go
new file mode 100644
index 000000000..7db8a3467
--- /dev/null
+++ b/bundle/config/validate/no_workspace_prefix_used_test.go
@@ -0,0 +1,78 @@
+package validate
+
+import (
+	"context"
+	"testing"
+
+	"github.com/databricks/cli/bundle"
+	"github.com/databricks/cli/bundle/config"
+	"github.com/databricks/cli/bundle/config/resources"
+	"github.com/databricks/cli/libs/diag"
+	"github.com/databricks/databricks-sdk-go/service/compute"
+	"github.com/databricks/databricks-sdk-go/service/jobs"
+	"github.com/stretchr/testify/require"
+)
+
+func TestNoWorkspacePrefixUsed(t *testing.T) {
+	b := &bundle.Bundle{
+		Config: config.Root{
+			Workspace: config.Workspace{
+				RootPath:     "/Workspace/Users/test",
+				ArtifactPath: "/Workspace/Users/test/artifacts",
+				FilePath:     "/Workspace/Users/test/files",
+				StatePath:    "/Workspace/Users/test/state",
+			},
+
+			Resources: config.Resources{
+				Jobs: map[string]*resources.Job{
+					"test_job": {
+						JobSettings: &jobs.JobSettings{
+							Tasks: []jobs.Task{
+								{
+									SparkPythonTask: &jobs.SparkPythonTask{
+										PythonFile: "/Workspace/${workspace.root_path}/file1.py",
+									},
+								},
+								{
+									NotebookTask: &jobs.NotebookTask{
+										NotebookPath: "/Workspace/${workspace.file_path}/notebook1",
+									},
+									Libraries: []compute.Library{
+										{
+											Jar: "/Workspace/${workspace.artifact_path}/jar1.jar",
+										},
+									},
+								},
+								{
+									NotebookTask: &jobs.NotebookTask{
+										NotebookPath: "${workspace.file_path}/notebook2",
+									},
+									Libraries: []compute.Library{
+										{
+											Jar: "${workspace.artifact_path}/jar2.jar",
+										},
+									},
+								},
+							},
+						},
+					},
+				},
+			},
+		},
+	}
+
+	diags := bundle.Apply(context.Background(), b, NoWorkspacePrefixUsed())
+	require.Len(t, diags, 3)
+
+	expectedErrors := map[string]bool{
+		"/Workspace/${workspace.root_path} used in the remote path /Workspace/${workspace.root_path}/file1.py. Please change to use ${workspace.root_path}/file1.py instead":             true,
+		"/Workspace/${workspace.file_path} used in the remote path /Workspace/${workspace.file_path}/notebook1. Please change to use ${workspace.file_path}/notebook1 instead":           true,
+		"/Workspace/${workspace.artifact_path} used in the remote path /Workspace/${workspace.artifact_path}/jar1.jar. Please change to use ${workspace.artifact_path}/jar1.jar instead": true,
+	}
+
+	for _, d := range diags {
+		require.Equal(t, d.Severity, diag.Error)
+		require.Contains(t, expectedErrors, d.Summary)
+		delete(expectedErrors, d.Summary)
+	}
+}
diff --git a/bundle/config/workspace.go b/bundle/config/workspace.go
index efc5caa66..c57b96d72 100644
--- a/bundle/config/workspace.go
+++ b/bundle/config/workspace.go
@@ -47,7 +47,7 @@ type Workspace struct {
 
 	// Remote workspace base path for deployment state, for artifacts, as synchronization target.
 	// This defaults to "~/.bundle/${bundle.name}/${bundle.target}" where "~" expands to
-	// the current user's home directory in the workspace (e.g. `/Users/jane@doe.com`).
+	// the current user's home directory in the workspace (e.g. `/Workspace/Users/jane@doe.com`).
 	RootPath string `json:"root_path,omitempty"`
 
 	// Remote workspace path to synchronize local files to.
diff --git a/bundle/phases/initialize.go b/bundle/phases/initialize.go
index fbb47d8e9..c8b96579f 100644
--- a/bundle/phases/initialize.go
+++ b/bundle/phases/initialize.go
@@ -45,6 +45,8 @@ func Initialize() bundle.Mutator {
 			mutator.DefineDefaultWorkspacePaths(),
 			mutator.PrependWorkspacePrefix(),
 
+			validate.NoWorkspacePrefixUsed(),
+
 			mutator.SetVariables(),
 			// Intentionally placed before ResolveVariableReferencesInLookup, ResolveResourceReferences,
 			// ResolveVariableReferencesInComplexVariables and ResolveVariableReferences.
diff --git a/internal/bundle/deploy_test.go b/internal/bundle/deploy_test.go
index 736c880db..885435855 100644
--- a/internal/bundle/deploy_test.go
+++ b/internal/bundle/deploy_test.go
@@ -236,7 +236,7 @@ func TestAccDeployBasicBundleLogs(t *testing.T) {
 
 	stdout, stderr := blackBoxRun(t, root, "bundle", "deploy")
 	assert.Equal(t, strings.Join([]string{
-		fmt.Sprintf("Uploading bundle files to /Users/%s/.bundle/%s/files...", currentUser.UserName, uniqueId),
+		fmt.Sprintf("Uploading bundle files to /Workspace/Users/%s/.bundle/%s/files...", currentUser.UserName, uniqueId),
 		"Deploying resources...",
 		"Updating deployment state...",
 		"Deployment complete!\n",
diff --git a/libs/template/templates/dbt-sql/template/{{.project_name}}/databricks.yml.tmpl b/libs/template/templates/dbt-sql/template/{{.project_name}}/databricks.yml.tmpl
index f96ce4fe6..5594749a9 100644
--- a/libs/template/templates/dbt-sql/template/{{.project_name}}/databricks.yml.tmpl
+++ b/libs/template/templates/dbt-sql/template/{{.project_name}}/databricks.yml.tmpl
@@ -24,8 +24,8 @@ targets:
     mode: production
     workspace:
       host: {{workspace_host}}
-      # We explicitly specify /Users/{{user_name}} to make sure we only have a single copy.
-      root_path: /Users/{{user_name}}/.bundle/${bundle.name}/${bundle.target}
+      # We explicitly specify /Workspace/Users/{{user_name}} to make sure we only have a single copy.
+      root_path: /Workspace/Users/{{user_name}}/.bundle/${bundle.name}/${bundle.target}
     permissions:
       - {{if is_service_principal}}service_principal{{else}}user{{end}}_name: {{user_name}}
         level: CAN_MANAGE
diff --git a/libs/template/templates/default-python/template/{{.project_name}}/databricks.yml.tmpl b/libs/template/templates/default-python/template/{{.project_name}}/databricks.yml.tmpl
index 8544dc834..c42b822a8 100644
--- a/libs/template/templates/default-python/template/{{.project_name}}/databricks.yml.tmpl
+++ b/libs/template/templates/default-python/template/{{.project_name}}/databricks.yml.tmpl
@@ -21,8 +21,8 @@ targets:
     mode: production
     workspace:
       host: {{workspace_host}}
-      # We explicitly specify /Users/{{user_name}} to make sure we only have a single copy.
-      root_path: /Users/{{user_name}}/.bundle/${bundle.name}/${bundle.target}
+      # We explicitly specify /Workspace/Users/{{user_name}} to make sure we only have a single copy.
+      root_path: /Workspace/Users/{{user_name}}/.bundle/${bundle.name}/${bundle.target}
     permissions:
       - {{if is_service_principal}}service_principal{{else}}user{{end}}_name: {{user_name}}
         level: CAN_MANAGE
diff --git a/libs/template/templates/default-python/template/{{.project_name}}/resources/{{.project_name}}.pipeline.yml.tmpl b/libs/template/templates/default-python/template/{{.project_name}}/resources/{{.project_name}}.pipeline.yml.tmpl
index bf4690461..50e5ad97c 100644
--- a/libs/template/templates/default-python/template/{{.project_name}}/resources/{{.project_name}}.pipeline.yml.tmpl
+++ b/libs/template/templates/default-python/template/{{.project_name}}/resources/{{.project_name}}.pipeline.yml.tmpl
@@ -15,4 +15,4 @@ resources:
             path: ../src/dlt_pipeline.ipynb
 
       configuration:
-        bundle.sourcePath: /Workspace/${workspace.file_path}/src
+        bundle.sourcePath: ${workspace.file_path}/src
diff --git a/libs/template/templates/default-sql/template/{{.project_name}}/databricks.yml.tmpl b/libs/template/templates/default-sql/template/{{.project_name}}/databricks.yml.tmpl
index 55c1aae4a..51d03e99a 100644
--- a/libs/template/templates/default-sql/template/{{.project_name}}/databricks.yml.tmpl
+++ b/libs/template/templates/default-sql/template/{{.project_name}}/databricks.yml.tmpl
@@ -41,8 +41,8 @@ targets:
     mode: production
     workspace:
       host: {{workspace_host}}
-      # We explicitly specify /Users/{{user_name}} to make sure we only have a single copy.
-      root_path: /Users/{{user_name}}/.bundle/${bundle.name}/${bundle.target}
+      # We explicitly specify /Workspace/Users/{{user_name}} to make sure we only have a single copy.
+      root_path: /Workspace/Users/{{user_name}}/.bundle/${bundle.name}/${bundle.target}
     variables:
       warehouse_id: {{index ((regexp "[^/]+$").FindStringSubmatch .http_path) 0}}
       catalog: {{.default_catalog}}