diff --git a/pkg/sources/github/connector.go b/pkg/sources/github/connector.go
index 494ab5d18..3f460295b 100644
--- a/pkg/sources/github/connector.go
+++ b/pkg/sources/github/connector.go
@@ -18,6 +18,8 @@ import (
 const (
 	cloudV3Endpoint      = "https://api.github.com"
 	cloudGraphqlEndpoint = "https://api.github.com/graphql" // https://docs.github.com/en/graphql/guides/forming-calls-with-graphql#the-graphql-endpoint
+
+	gheCloudSuffix = ".ghe.com"
 )
 
 // Connector abstracts over the authenticated ways to interact with GitHub: cloning and API operations.
@@ -34,6 +36,81 @@ type Connector interface {
 	Clone(ctx context.Context, repoURL string, args ...string) (string, *gogit.Repository, error)
 }
 
+// isGHECloud returns true if the endpoint is a GHE.com instance
+// (GHEC with data residency). GHE.com uses the same root-level API layout as
+// api.github.com, NOT the GHES /api/v3/ layout.
+//
+// Examples:
+//
+//	https://api.company.ghe.com   -> true
+//	https://company.ghe.com       -> true  (web URL; user might pass this)
+//	https://github.mycompany.com -> false (GHES)
+//	https://api.github.com       -> false (regular github.com)
+func isGHECloud(endpoint string) bool {
+	u, err := url.Parse(strings.TrimRight(endpoint, "/"))
+	if err != nil {
+		return false
+	}
+	return strings.HasSuffix(strings.ToLower(u.Hostname()), gheCloudSuffix)
+}
+
+// normalizeGHECloudAPIEndpoint ensures the endpoint points to the API subdomain
+// with a trailing slash (required by go-github's BaseURL).
+//
+// On GHE.com the web UI lives at SUBDOMAIN.ghe.com while the API lives at
+// api.SUBDOMAIN.ghe.com. Users may pass either form.
+//
+//	https://company.ghe.com       -> https://api.company.ghe.com/
+//	https://company.ghe.com/      -> https://api.company.ghe.com/
+//	https://api.company.ghe.com   -> https://api.company.ghe.com/
+//	https://api.company.ghe.com/  -> https://api.company.ghe.com/
+func normalizeGHECloudAPIEndpoint(endpoint string) (string, error) {
+	u, err := url.Parse(strings.TrimRight(endpoint, "/"))
+	if err != nil {
+		return "", fmt.Errorf("invalid GHE.com endpoint URL: %w", err)
+	}
+
+	host := u.Hostname()
+	port := u.Port()
+
+	// If user passed the web URL (company.ghe.com), prepend "api."
+	if !strings.HasPrefix(strings.ToLower(host), "api.") {
+		host = "api." + host
+	}
+
+	if port != "" {
+		u.Host = host + ":" + port
+	} else {
+		u.Host = host
+	}
+
+	// go-github requires a trailing slash on BaseURL.
+	u.Path = "/"
+
+	return u.String(), nil
+}
+
+// createGHECloudClient creates a go-github client configured for GHE.com.
+// GHE.com serves its REST API at the root of api.SUBDOMAIN.ghe.com (same
+// layout as api.github.com), so we must NOT use WithEnterpriseURLs which
+// would append /api/v3/.
+func createGHECloudClient(httpClient *http.Client, apiEndpoint string) (*github.Client, error) {
+	apiURL, err := normalizeGHECloudAPIEndpoint(apiEndpoint)
+	if err != nil {
+		return nil, err
+	}
+
+	parsedURL, err := url.Parse(apiURL)
+	if err != nil {
+		return nil, fmt.Errorf("failed to parse GHE.com API URL: %w", err)
+	}
+
+	client := github.NewClient(httpClient)
+	client.BaseURL = parsedURL
+	client.UploadURL = parsedURL
+	return client, nil
+}
+
 func newConnector(ctx context.Context, source *Source) (Connector, error) {
 	apiEndpoint := canonicalAPIEndpoint(source.conn.Endpoint)
 
@@ -60,27 +137,44 @@ func createAPIClient(ctx context.Context, httpClient *http.Client, apiEndpoint s
 	ctx.Logger().V(2).Info("Creating API client", "url", apiEndpoint)
 
 	// If we're using public GitHub, make a regular client.
-	// Otherwise, make an enterprise client.
 	if strings.EqualFold(apiEndpoint, cloudV3Endpoint) {
 		return github.NewClient(httpClient), nil
 	}
 
+	// GHE.com (GHEC with data residency) serves its API at the root level
+	// (like api.github.com), NOT under /api/v3/.
+	if isGHECloud(apiEndpoint) {
+		return createGHECloudClient(httpClient, apiEndpoint)
+	}
+
+	// GHES (self-hosted) — WithEnterpriseURLs appends /api/v3/ and /api/uploads/.
 	return github.NewClient(httpClient).WithEnterpriseURLs(apiEndpoint, apiEndpoint)
 }
 
 func createGraphqlClient(ctx context.Context, client *http.Client, apiEndpoint string) (*githubv4.Client, error) {
 	var graphqlEndpoint string
-	if apiEndpoint == cloudV3Endpoint {
+	switch {
+	case apiEndpoint == cloudV3Endpoint:
 		graphqlEndpoint = cloudGraphqlEndpoint
-	} else {
-		// Use the root endpoint for the host.
+
+	case isGHECloud(apiEndpoint):
+		// GHE.com: GraphQL lives at the root level, same as api.github.com.
+		// https://api.SUBDOMAIN.ghe.com/graphql
+		apiURL, err := normalizeGHECloudAPIEndpoint(apiEndpoint)
+		if err != nil {
+			return nil, fmt.Errorf("error normalizing GHE.com endpoint: %w", err)
+		}
+		graphqlEndpoint = strings.TrimRight(apiURL, "/") + "/graphql"
+
+	default:
+		// GHES: GraphQL lives under /api/graphql.
 		// https://docs.github.com/en/enterprise-server@3.11/graphql/guides/introduction-to-graphql
 		parsedURL, err := url.Parse(apiEndpoint)
 		if err != nil {
 			return nil, fmt.Errorf("error parsing URL: %w", err)
 		}
 
-		// GitHub Enterprise uses `/api/v3` for the base. (https://github.com/google/go-github/issues/958)
+		// GitHub Enterprise Server uses `/api/v3` for the base. (https://github.com/google/go-github/issues/958)
 		// Swap it, and anything before `/api`, with GraphQL.
 		before, _ := strings.CutSuffix(parsedURL.Path, "/api/v3")
 		parsedURL.Path = before + "/api/graphql"
diff --git a/pkg/sources/github/connector_app.go b/pkg/sources/github/connector_app.go
index 0b66c4684..cef1567db 100644
--- a/pkg/sources/github/connector_app.go
+++ b/pkg/sources/github/connector_app.go
@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"net/http"
 	"strconv"
+	"strings"
 	"sync"
 
 	"github.com/bradleyfalzon/ghinstallation/v2"
@@ -273,8 +274,10 @@ func (c *appConnector) createAPIClientForInstallation(installationID int64) (*gi
 		return nil, fmt.Errorf("could not create app transport for installation %d: %w", installationID, err)
 	}
 
+	// NewFromAppsTransport inherits BaseURL from appsTransport, which
+	// newAppsTransport already set correctly (incl. GHE.com). Don't override it
+	// with the raw endpoint here or GHE.com token refresh would 401.
 	transport := ghinstallation.NewFromAppsTransport(appsTransport, installationID)
-	transport.BaseURL = c.apiEndpoint
 
 	client, err := newGitHubClientWithTransport(c.apiEndpoint, transport)
 	if err != nil {
@@ -289,12 +292,41 @@ func newAppsTransport(apiEndpoint string, appID int64, privateKey []byte) (*ghin
 	if err != nil {
 		return nil, err
 	}
-	appsTransport.BaseURL = apiEndpoint
+
+	// ghinstallation uses BaseURL to build the token exchange URL
+	// {BaseURL}/app/installations/{id}/access_tokens. For GHE.com this must be
+	// the api.SUBDOMAIN.ghe.com base with no /api/v3 and no trailing slash
+	// (which ghinstallation does not expect), otherwise token refresh 401s.
+	baseURL, err := appsBaseURL(apiEndpoint)
+	if err != nil {
+		return nil, err
+	}
+	appsTransport.BaseURL = baseURL
 	return appsTransport, nil
 }
 
+// appsBaseURL returns the BaseURL that ghinstallation transports should use for
+// token exchange/refresh. For GHE.com it resolves to the api.* subdomain with
+// the trailing slash trimmed; for github.com and GHES it is the endpoint as-is.
+func appsBaseURL(apiEndpoint string) (string, error) {
+	if isGHECloud(apiEndpoint) {
+		normalizedURL, err := normalizeGHECloudAPIEndpoint(apiEndpoint)
+		if err != nil {
+			return "", fmt.Errorf("could not normalize GHE.com endpoint: %w", err)
+		}
+		return strings.TrimRight(normalizedURL, "/"), nil
+	}
+	return apiEndpoint, nil
+}
+
 func newGitHubClientWithTransport(apiEndpoint string, transport http.RoundTripper) (*github.Client, error) {
 	httpClient := common.RetryableHTTPClientTimeout(githubHTTPTimeoutSeconds)
 	httpClient.Transport = transport
+
+	// GHE.com (GHEC with data residency) serves its REST API at the root of
+	// api.SUBDOMAIN.ghe.com (like api.github.com), NOT under the GHES /api/v3 path.
+	if isGHECloud(apiEndpoint) {
+		return createGHECloudClient(httpClient, apiEndpoint)
+	}
 	return github.NewClient(httpClient).WithEnterpriseURLs(apiEndpoint, apiEndpoint)
 }
diff --git a/pkg/sources/github/connector_token.go b/pkg/sources/github/connector_token.go
index fc878c07e..1e4d23417 100644
--- a/pkg/sources/github/connector_token.go
+++ b/pkg/sources/github/connector_token.go
@@ -49,11 +49,16 @@ func NewTokenConnector(ctx context.Context, apiEndpoint, token, clonePath string
 		return nil, fmt.Errorf("error creating GraphQL client: %w", err)
 	}
 
+	// Treat both GHES and GHE.com as "enterprise" for enumeration purposes.
+	// GHE.com (GHEC with data residency) is a dedicated enterprise environment
+	// with EMU, so enterprise-level enumeration (e.g., addAllVisibleOrgs) applies.
+	isEnterprise := !strings.EqualFold(apiEndpoint, cloudV3Endpoint)
+
 	return &tokenConnector{
 		apiClient:          apiClient,
 		graphqlClient:      graphqlClient,
 		token:              token,
-		isGitHubEnterprise: !strings.EqualFold(apiEndpoint, cloudV3Endpoint),
+		isGitHubEnterprise: isEnterprise,
 		handleRateLimit:    handleRateLimit,
 		authInUrl:          authInUrl,
 		clonePath:          clonePath,
diff --git a/pkg/sources/github/github_test.go b/pkg/sources/github/github_test.go
index 64f48b283..906924016 100644
--- a/pkg/sources/github/github_test.go
+++ b/pkg/sources/github/github_test.go
@@ -366,6 +366,51 @@ func TestAddReposByApp(t *testing.T) {
 	assert.True(t, gock.IsDone())
 }
 
+// TestAppConnector_EnterpriseBaseURL verifies that GitHub App authentication
+// correctly sets the BaseURL on the internal AppsTransport for token refresh.
+// This is critical for GitHub Enterprise Server and GHEC with Data Residency.
+// Without this fix, token refresh requests would go to api.github.com instead
+// of the configured enterprise endpoint.
+func TestAppConnector_EnterpriseBaseURL(t *testing.T) {
+	privateKey := createPrivateKey()
+	enterpriseEndpoint := "https://api.example.ghe.com"
+
+	connector, err := NewAppConnector(
+		context.Background(),
+		enterpriseEndpoint,
+		&credentialspb.GitHubApp{
+			PrivateKey:     privateKey,
+			InstallationId: "1337",
+			AppId:          "4141",
+		})
+	require.NoError(t, err)
+
+	appConn, ok := connector.(*appConnector)
+	require.True(t, ok, "connector should be an appConnector")
+
+	// Get the HTTP client's transport, which should be a ghinstallation.Transport
+	transport := appConn.APIClient().Client().Transport
+
+	// Use reflection to access the Transport's BaseURL field
+	transportVal := reflect.ValueOf(transport).Elem()
+	baseURLField := transportVal.FieldByName("BaseURL")
+	require.True(t, baseURLField.IsValid(), "Transport should have a BaseURL field")
+	assert.Equal(t, enterpriseEndpoint, baseURLField.String(),
+		"Transport.BaseURL should be set to enterprise endpoint")
+
+	// Use reflection to access the internal appsTransport and verify its BaseURL
+	// This is the critical check - the internal AppsTransport is used for token refresh
+	appsTransportField := transportVal.FieldByName("appsTransport")
+	require.True(t, appsTransportField.IsValid(), "Transport should have an appsTransport field")
+
+	// Access the BaseURL of the internal AppsTransport
+	appsTransportVal := appsTransportField.Elem()
+	appsBaseURLField := appsTransportVal.FieldByName("BaseURL")
+	require.True(t, appsBaseURLField.IsValid(), "AppsTransport should have a BaseURL field")
+	assert.Equal(t, enterpriseEndpoint, appsBaseURLField.String(),
+		"AppsTransport.BaseURL should be set to enterprise endpoint")
+}
+
 func TestAddOrgsByUser(t *testing.T) {
 	defer gock.Off()
 
@@ -2737,3 +2782,182 @@ func TestSource_ExcludeArchivedForkInteraction(t *testing.T) {
 		})
 	}
 }
+
+func TestIsGHECloud(t *testing.T) {
+	tests := []struct {
+		name     string
+		endpoint string
+		want     bool
+	}{
+		// GHE.com endpoints — should return true
+		{"api subdomain", "https://api.company.ghe.com", true},
+		{"web subdomain", "https://company.ghe.com", true},
+		{"api subdomain trailing slash", "https://api.company.ghe.com/", true},
+		{"web subdomain trailing slash", "https://company.ghe.com/", true},
+		{"uppercase", "https://API.company.GHE.COM", true},
+		{"mixed case", "https://Api.company.Ghe.Com/", true},
+		{"deep subdomain", "https://api.team.company.ghe.com", true},
+
+		// GHES endpoints — should return false
+		{"ghes custom domain", "https://github.mycompany.com", false},
+		{"ghes with path", "https://github.mycompany.com/api/v3", false},
+		{"ghes internal", "https://github.internal.corp.com", false},
+
+		// github.com — should return false
+		{"cloud api", "https://api.github.com", false},
+		{"cloud web", "https://github.com", false},
+
+		// Edge cases — should return false
+		{"empty string", "", false},
+		{"localhost", "http://localhost:8080", false},
+		{"malicious suffix", "https://notghe.com", false},
+		{"partial match", "https://api.fakeghe.com.evil.com", false},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			got := isGHECloud(tt.endpoint)
+			if got != tt.want {
+				t.Errorf("isGHECloud(%q) = %v, want %v", tt.endpoint, got, tt.want)
+			}
+		})
+	}
+}
+
+func TestNormalizeGHECloudAPIEndpoint(t *testing.T) {
+	tests := []struct {
+		name    string
+		input   string
+		want    string
+		wantErr bool
+	}{
+		{
+			name:  "web URL to API URL",
+			input: "https://company.ghe.com",
+			want:  "https://api.company.ghe.com/",
+		},
+		{
+			name:  "web URL with trailing slash",
+			input: "https://company.ghe.com/",
+			want:  "https://api.company.ghe.com/",
+		},
+		{
+			name:  "api URL already correct",
+			input: "https://api.company.ghe.com",
+			want:  "https://api.company.ghe.com/",
+		},
+		{
+			name:  "api URL with trailing slash",
+			input: "https://api.company.ghe.com/",
+			want:  "https://api.company.ghe.com/",
+		},
+		{
+			name:  "preserves port",
+			input: "http://company.ghe.com:8080",
+			want:  "http://api.company.ghe.com:8080/",
+		},
+		{
+			name:  "api with port",
+			input: "http://api.company.ghe.com:8080",
+			want:  "http://api.company.ghe.com:8080/",
+		},
+		{
+			name:  "strips path",
+			input: "https://company.ghe.com/some/path",
+			want:  "https://api.company.ghe.com/",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			got, err := normalizeGHECloudAPIEndpoint(tt.input)
+			if (err != nil) != tt.wantErr {
+				t.Errorf("normalizeGHECloudAPIEndpoint(%q) error = %v, wantErr %v", tt.input, err, tt.wantErr)
+				return
+			}
+			if got != tt.want {
+				t.Errorf("normalizeGHECloudAPIEndpoint(%q) = %q, want %q", tt.input, got, tt.want)
+			}
+		})
+	}
+}
+
+func TestCreateAPIClient_GHECloud_NoAPIV3(t *testing.T) {
+	// The most critical test: GHE.com clients must NOT have /api/v3/ in their BaseURL.
+	endpoints := []string{
+		"https://api.company.ghe.com",
+		"https://company.ghe.com",
+		"https://api.company.ghe.com/",
+		"https://company.ghe.com/",
+	}
+
+	for _, endpoint := range endpoints {
+		t.Run(endpoint, func(t *testing.T) {
+			client, err := createGHECloudClient(http.DefaultClient, endpoint)
+			if err != nil {
+				t.Fatalf("createGHECloudClient(%q) unexpected error: %v", endpoint, err)
+			}
+
+			baseURL := client.BaseURL.String()
+
+			// Must NOT contain /api/v3
+			if strings.Contains(baseURL, "/api/v3") {
+				t.Errorf("GHE.com client BaseURL must not contain /api/v3/, got: %s", baseURL)
+			}
+
+			// Must point to api.company.ghe.com
+			if client.BaseURL.Hostname() != "api.company.ghe.com" {
+				t.Errorf("expected hostname api.company.ghe.com, got: %s", client.BaseURL.Hostname())
+			}
+
+			// Must have trailing slash
+			if !strings.HasSuffix(baseURL, "/") {
+				t.Errorf("BaseURL must have trailing slash, got: %s", baseURL)
+			}
+		})
+	}
+}
+
+func TestCreateGraphqlClient_GHECloud(t *testing.T) {
+	// GHE.com GraphQL should be at /graphql, NOT /api/graphql.
+	// We can't easily inspect the URL from the githubv4.Client,
+	// so we test the URL construction logic indirectly by checking
+	// the normalized endpoint.
+	apiURL, err := normalizeGHECloudAPIEndpoint("https://company.ghe.com")
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	graphqlURL := strings.TrimRight(apiURL, "/") + "/graphql"
+	expected := "https://api.company.ghe.com/graphql"
+
+	if graphqlURL != expected {
+		t.Errorf("GHE.com GraphQL URL = %q, want %q", graphqlURL, expected)
+	}
+}
+
+func TestCreateAPIClient_GHES_HasAPIV3(t *testing.T) {
+	// GHES clients SHOULD have /api/v3/ — make sure we didn't break that.
+	// Note: WithEnterpriseURLs returns an error for invalid URLs, but for
+	// valid ones it appends /api/v3/.
+	client, err := createAPIClient(context.Background(), http.DefaultClient, "https://github.mycompany.com")
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	if !strings.Contains(client.BaseURL.String(), "/api/v3") {
+		t.Errorf("GHES client BaseURL should contain /api/v3/, got: %s", client.BaseURL.String())
+	}
+}
+
+func TestCreateAPIClient_CloudGitHub(t *testing.T) {
+	// Regular github.com should use the default client (api.github.com).
+	client, err := createAPIClient(context.Background(), http.DefaultClient, cloudV3Endpoint)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	if client.BaseURL.String() != "https://api.github.com/" {
+		t.Errorf("expected https://api.github.com/, got: %s", client.BaseURL.String())
+	}
+}