diff --git a/.beads/config.yaml b/.beads/config.yaml
index 90618901..a488e63c 100644
--- a/.beads/config.yaml
+++ b/.beads/config.yaml
@@ -3,6 +3,11 @@
 # All settings can also be set via environment variables (BD_* prefix)
 # or overridden with command-line flags
 
+# Issue prefix for this repository (used by bd init)
+# If not set, bd init will auto-detect from directory name
+# Example: issue-prefix: "myproject" creates issues like "myproject-1", "myproject-2", etc.
+# issue-prefix: ""
+
 # Use no-db mode: load from JSONL, no SQLite, write back after each command
 # When true, bd will use .beads/issues.jsonl as the source of truth
 # instead of SQLite database
diff --git a/cmd/bd/init.go b/cmd/bd/init.go
index 1c4971c7..b04481be 100644
--- a/cmd/bd/init.go
+++ b/cmd/bd/init.go
@@ -10,6 +10,7 @@ import (
 
 	"github.com/fatih/color"
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 )
 
@@ -24,6 +25,12 @@ With --no-db: creates .beads/ directory and nodb_prefix.txt file instead of SQLi
 		prefix, _ := cmd.Flags().GetString("prefix")
 		quiet, _ := cmd.Flags().GetBool("quiet")
 
+		// Initialize config (PersistentPreRun doesn't run for init command)
+		if err := config.Initialize(); err != nil {
+			fmt.Fprintf(os.Stderr, "Warning: failed to initialize config: %v\n", err)
+			// Non-fatal - continue with defaults
+		}
+
 		// Check BEADS_DB environment variable if --db flag not set
 		// (PersistentPreRun doesn't run for init command)
 		if dbPath == "" {
@@ -32,6 +39,12 @@ With --no-db: creates .beads/ directory and nodb_prefix.txt file instead of SQLi
 			}
 		}
 
+		// Determine prefix with precedence: flag > config > auto-detect
+		if prefix == "" {
+			// Try to get from config file
+			prefix = config.GetString("issue-prefix")
+		}
+
 		if prefix == "" {
 			// Auto-detect from directory name
 			cwd, err := os.Getwd()
diff --git a/cmd/bd/nodb.go b/cmd/bd/nodb.go
index 74309f4b..a7da98aa 100644
--- a/cmd/bd/nodb.go
+++ b/cmd/bd/nodb.go
@@ -9,6 +9,7 @@ import (
 	"path/filepath"
 	"strings"
 
+	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/storage/memory"
 	"github.com/steveyegge/beads/internal/types"
 )
@@ -111,8 +112,9 @@ func loadIssuesFromJSONL(path string) ([]*types.Issue, error) {
 // detectPrefix detects the issue prefix to use in --no-db mode
 // Priority:
 // 1. .beads/nodb_prefix.txt file (if exists)
-// 2. Common prefix from existing issues (if all share same prefix)
-// 3. Current directory name (fallback)
+// 2. issue-prefix from config.yaml (if set)
+// 3. Common prefix from existing issues (if all share same prefix)
+// 4. Current directory name (fallback)
 func detectPrefix(beadsDir string, memStore *memory.MemoryStorage) (string, error) {
 	// Check for nodb_prefix.txt
 	prefixFile := filepath.Join(beadsDir, "nodb_prefix.txt")
@@ -123,6 +125,12 @@ func detectPrefix(beadsDir string, memStore *memory.MemoryStorage) (string, erro
 		}
 	}
 
+	// Check config.yaml for issue-prefix
+	configPrefix := config.GetString("issue-prefix")
+	if configPrefix != "" {
+		return configPrefix, nil
+	}
+
 	// Check existing issues for common prefix
 	issues := memStore.GetAllIssues()
 	if len(issues) > 0 {
diff --git a/internal/config/config.go b/internal/config/config.go
index ce8c4e6e..a806380e 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -74,6 +74,7 @@ func Initialize() error {
 	v.SetDefault("no-db", false)
 	v.SetDefault("db", "")
 	v.SetDefault("actor", "")
+	v.SetDefault("issue-prefix", "")
 	
 	// Additional environment variables (not prefixed with BD_)
 	// These are bound explicitly for backward compatibility