diff --git a/internal/importer/importer.go b/internal/importer/importer.go
index 5d21c75f..47ecb8f0 100644
--- a/internal/importer/importer.go
+++ b/internal/importer/importer.go
@@ -7,6 +7,7 @@ import (
 	"sort"
 	"strings"
 
+	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/linear"
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
@@ -106,6 +107,12 @@ func ImportIssues(ctx context.Context, dbPath string, store storage.Storage, iss
 		defer func() { _ = sqliteStore.Close() }()
 	}
 
+	// GH#686: In multi-repo mode, skip prefix validation for all issues.
+	// Issues from additional repos have their own prefixes which are expected and correct.
+	if config.GetMultiRepoConfig() != nil && !opts.SkipPrefixValidation {
+		opts.SkipPrefixValidation = true
+	}
+
 	// Clear export_hashes before import to prevent staleness (bd-160)
 	// Import operations may add/update issues, so export_hashes entries become invalid
 	if !opts.DryRun {
@@ -208,6 +215,12 @@ func handlePrefixMismatch(ctx context.Context, sqliteStore *sqlite.SQLiteStorage
 
 	result.ExpectedPrefix = configuredPrefix
 
+	// GH#686: In multi-repo mode, allow all prefixes (nil = allow all)
+	allowedPrefixes := buildAllowedPrefixSet(configuredPrefix)
+	if allowedPrefixes == nil {
+		return issues, nil
+	}
+
 	// Analyze prefixes in imported issues
 	// Track tombstones separately - they don't count as "real" mismatches (bd-6pni)
 	tombstoneMismatchPrefixes := make(map[string]int)
@@ -219,7 +232,7 @@ func handlePrefixMismatch(ctx context.Context, sqliteStore *sqlite.SQLiteStorage
 
 	for _, issue := range issues {
 		prefix := utils.ExtractIssuePrefix(issue.ID)
-		if prefix != configuredPrefix {
+		if !allowedPrefixes[prefix] {
 			if issue.IsTombstone() {
 				tombstoneMismatchPrefixes[prefix]++
 				tombstonesToRemove = append(tombstonesToRemove, issue.ID)
@@ -939,3 +952,12 @@ func validateNoDuplicateExternalRefs(issues []*types.Issue, clearDuplicates bool
 
 	return nil
 }
+
+// buildAllowedPrefixSet returns allowed prefixes, or nil to allow all (GH#686).
+// In multi-repo mode, additional repos have their own prefixes - allow all.
+func buildAllowedPrefixSet(primaryPrefix string) map[string]bool {
+	if config.GetMultiRepoConfig() != nil {
+		return nil // Multi-repo: allow all prefixes
+	}
+	return map[string]bool{primaryPrefix: true}
+}
diff --git a/internal/importer/importer_test.go b/internal/importer/importer_test.go
index 37540e51..e11634b0 100644
--- a/internal/importer/importer_test.go
+++ b/internal/importer/importer_test.go
@@ -9,6 +9,7 @@ import (
 	"testing"
 	"time"
 
+	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
 )
@@ -1477,3 +1478,89 @@ func TestImportMixedPrefixMismatch(t *testing.T) {
 		t.Errorf("Error should mention prefix mismatch, got: %v", err)
 	}
 }
+
+// TestMultiRepoPrefixValidation tests GH#686: multi-repo allows foreign prefixes.
+func TestMultiRepoPrefixValidation(t *testing.T) {
+	if err := config.Initialize(); err != nil {
+		t.Fatalf("Failed to initialize config: %v", err)
+	}
+
+	ctx := context.Background()
+	tmpDB := t.TempDir() + "/test.db"
+	store, err := sqlite.New(ctx, tmpDB)
+	if err != nil {
+		t.Fatalf("Failed to create store: %v", err)
+	}
+	defer store.Close()
+
+	if err := store.SetConfig(ctx, "issue_prefix", "primary"); err != nil {
+		t.Fatalf("Failed to set prefix: %v", err)
+	}
+
+	t.Run("single-repo mode rejects foreign prefixes", func(t *testing.T) {
+		config.Set("repos.primary", "")
+		config.Set("repos.additional", nil)
+
+		issues := []*types.Issue{
+			{
+				ID:        "primary-1",
+				Title:     "Primary issue",
+				Status:    types.StatusOpen,
+				Priority:  2,
+				IssueType: types.TypeTask,
+			},
+			{
+				ID:        "foreign-1",
+				Title:     "Foreign issue",
+				Status:    types.StatusOpen,
+				Priority:  2,
+				IssueType: types.TypeTask,
+			},
+		}
+
+		_, err := ImportIssues(ctx, tmpDB, store, issues, Options{})
+		if err == nil {
+			t.Error("Expected error for foreign prefix in single-repo mode")
+		}
+		if err != nil && !strings.Contains(err.Error(), "prefix mismatch") {
+			t.Errorf("Expected prefix mismatch error, got: %v", err)
+		}
+	})
+
+	t.Run("multi-repo mode allows foreign prefixes", func(t *testing.T) {
+		config.Set("repos.primary", "/some/primary/path")
+		config.Set("repos.additional", []string{"/some/additional/path"})
+		defer func() {
+			config.Set("repos.primary", "")
+			config.Set("repos.additional", nil)
+		}()
+
+		issues := []*types.Issue{
+			{
+				ID:        "primary-abc1",
+				Title:     "Primary issue",
+				Status:    types.StatusOpen,
+				Priority:  2,
+				IssueType: types.TypeTask,
+			},
+			{
+				ID:         "foreign-xyz2",
+				Title:      "Foreign issue",
+				Status:     types.StatusOpen,
+				Priority:   2,
+				IssueType:  types.TypeTask,
+				SourceRepo: "~/code/foreign",
+			},
+		}
+
+		result, err := ImportIssues(ctx, tmpDB, store, issues, Options{
+			SkipPrefixValidation: false, // Verify auto-skip kicks in
+		})
+		if err != nil {
+			t.Errorf("Multi-repo mode should allow foreign prefixes, got error: %v", err)
+		}
+		if result != nil && result.PrefixMismatch {
+			t.Error("Multi-repo mode should not report prefix mismatch")
+		}
+	})
+}