diff --git a/pkg/workflow/github_tool_to_toolset_test.go b/pkg/workflow/github_tool_to_toolset_test.go
index 8815d1082d..47b2dd969c 100644
--- a/pkg/workflow/github_tool_to_toolset_test.go
+++ b/pkg/workflow/github_tool_to_toolset_test.go
@@ -291,8 +291,15 @@ func expandToolsetsForTesting(toolsets []string) []string {
 				}
 			}
 		case "all":
-			// Add all toolsets from the permissions map
+			// Add all toolsets from the permissions map, excluding those in GitHubToolsetsExcludedFromAll
+			excludedMap := make(map[string]bool, len(GitHubToolsetsExcludedFromAll))
+			for _, ex := range GitHubToolsetsExcludedFromAll {
+				excludedMap[ex] = true
+			}
 			for t := range toolsetPermissionsMap {
+				if excludedMap[t] {
+					continue
+				}
 				if !seenToolsets[t] {
 					expanded = append(expanded, t)
 					seenToolsets[t] = true
diff --git a/pkg/workflow/github_toolsets.go b/pkg/workflow/github_toolsets.go
index fad70f13e3..cc916b4fef 100644
--- a/pkg/workflow/github_toolsets.go
+++ b/pkg/workflow/github_toolsets.go
@@ -18,6 +18,11 @@ var DefaultGitHubToolsets = []string{"context", "repos", "issues", "pull_request
 // Use this when the workflow will run in GitHub Actions with GITHUB_TOKEN.
 var ActionFriendlyGitHubToolsets = []string{"context", "repos", "issues", "pull_requests"}
 
+// GitHubToolsetsExcludedFromAll defines toolsets that are NOT included when "all" is specified.
+// These toolsets require GitHub App-only permissions (e.g., vulnerability-alerts) that
+// cannot be granted via GITHUB_TOKEN, so they must be opted-in to explicitly.
+var GitHubToolsetsExcludedFromAll = []string{"dependabot"}
+
 // ParseGitHubToolsets parses the toolsets string and expands "default" and "all"
 // into their constituent toolsets. It handles comma-separated lists and deduplicates.
 func ParseGitHubToolsets(toolsetsStr string) []string {
@@ -58,9 +63,17 @@ func ParseGitHubToolsets(toolsetsStr string) []string {
 				}
 			}
 		case "all":
-			// Add all toolsets from the toolset permissions map
-			toolsetsLog.Printf("Expanding 'all' to %d toolsets from permissions map", len(toolsetPermissionsMap))
+			// Add all toolsets from the toolset permissions map, excluding those that
+			// require GitHub App-only permissions (see GitHubToolsetsExcludedFromAll).
+			toolsetsLog.Printf("Expanding 'all' to toolsets from permissions map (excluding %v)", GitHubToolsetsExcludedFromAll)
+			excludedMap := make(map[string]bool, len(GitHubToolsetsExcludedFromAll))
+			for _, ex := range GitHubToolsetsExcludedFromAll {
+				excludedMap[ex] = true
+			}
 			for t := range toolsetPermissionsMap {
+				if excludedMap[t] {
+					continue
+				}
 				if !seenToolsets[t] {
 					expanded = append(expanded, t)
 					seenToolsets[t] = true
diff --git a/pkg/workflow/github_toolsets_test.go b/pkg/workflow/github_toolsets_test.go
index fe4b5996e4..8fdb9ca433 100644
--- a/pkg/workflow/github_toolsets_test.go
+++ b/pkg/workflow/github_toolsets_test.go
@@ -70,9 +70,9 @@ func TestParseGitHubToolsets(t *testing.T) {
 			expected: []string{"context", "repos", "issues", "pull_requests", "discussions"},
 		},
 		{
-			name:  "All expands to all toolsets",
+			name:  "All expands to all toolsets except excluded ones",
 			input: "all",
-			// Should include all 19 toolsets - we'll check the count
+			// Should include all toolsets except those in GitHubToolsetsExcludedFromAll (e.g., dependabot)
 			expected: nil,
 		},
 		{
@@ -111,10 +111,21 @@ func TestParseGitHubToolsets(t *testing.T) {
 		t.Run(tt.name, func(t *testing.T) {
 			result := ParseGitHubToolsets(tt.input)
 
-			if tt.name == "All expands to all toolsets" {
-				// Check that all toolsets are present
-				if len(result) != len(toolsetPermissionsMap) {
-					t.Errorf("Expected %d toolsets for 'all', got %d", len(toolsetPermissionsMap), len(result))
+			if tt.name == "All expands to all toolsets except excluded ones" {
+				// Check that result is all toolsets minus excluded ones
+				expectedCount := len(toolsetPermissionsMap) - len(GitHubToolsetsExcludedFromAll)
+				if len(result) != expectedCount {
+					t.Errorf("Expected %d toolsets for 'all', got %d: %v", expectedCount, len(result), result)
+				}
+				// Verify excluded toolsets are not present
+				resultMap := make(map[string]bool)
+				for _, ts := range result {
+					resultMap[ts] = true
+				}
+				for _, ex := range GitHubToolsetsExcludedFromAll {
+					if resultMap[ex] {
+						t.Errorf("Excluded toolset %q should not be present in 'all' expansion", ex)
+					}
 				}
 				return
 			}
@@ -175,7 +186,7 @@ func TestParseGitHubToolsetsDeduplication(t *testing.T) {
 		{
 			name:     "All with duplicates",
 			input:    "all,repos,issues",
-			expected: len(toolsetPermissionsMap), // All toolsets, duplicates ignored
+			expected: len(toolsetPermissionsMap) - len(GitHubToolsetsExcludedFromAll), // All toolsets minus excluded, duplicates ignored
 		},
 	}
 
diff --git a/pkg/workflow/permissions_toolset_data.go b/pkg/workflow/permissions_toolset_data.go
index 80538014fa..60bf7534f7 100644
--- a/pkg/workflow/permissions_toolset_data.go
+++ b/pkg/workflow/permissions_toolset_data.go
@@ -109,6 +109,12 @@ func collectRequiredPermissions(toolsets []string, readOnly bool) map[Permission
 
 		// Add read permissions only (write tools are not considered for permission requirements)
 		for _, scope := range perms.ReadPermissions {
+			// Skip GitHub App-only permission scopes; these cannot be set via GITHUB_TOKEN
+			// and are validated separately in validateGitHubAppOnlyPermissions.
+			if IsGitHubAppOnlyScope(scope) {
+				permissionsValidationLog.Printf("Skipping GitHub App-only scope %s for toolset %s", scope, toolset)
+				continue
+			}
 			// Always require at least read access
 			if existing, found := required[scope]; !found || existing == PermissionNone {
 				required[scope] = PermissionRead
diff --git a/pkg/workflow/permissions_validator_test.go b/pkg/workflow/permissions_validator_test.go
index b871783e32..a4da6b7b03 100644
--- a/pkg/workflow/permissions_validator_test.go
+++ b/pkg/workflow/permissions_validator_test.go
@@ -89,12 +89,11 @@ func TestCollectRequiredPermissions(t *testing.T) {
 			},
 		},
 		{
-			name:     "Dependabot toolset requires vulnerability-alerts and security-events",
+			name:     "Dependabot toolset requires only security-events (vulnerability-alerts is GitHub App-only)",
 			toolsets: []string{"dependabot"},
 			readOnly: false,
 			expected: map[PermissionScope]PermissionLevel{
-				PermissionSecurityEvents:      PermissionRead,
-				PermissionVulnerabilityAlerts: PermissionRead,
+				PermissionSecurityEvents: PermissionRead,
 			},
 		},
 		{