diff --git a/scripts/bash/common.sh b/scripts/bash/common.sh
index 6931eccc8..c91f47ecc 100644
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -1,8 +1,19 @@
 #!/usr/bin/env bash
 # Common functions and variables for all scripts
 
-# Get repository root, with fallback for non-git repositories
+# Get repository root, prioritizing .specify over .git, with fallback for non-git repositories
 get_repo_root() {
+    # First check for .specify directory (highest priority)
+    local current_dir="$(pwd)"
+    while [ "$current_dir" != "/" ]; do
+        if [ -d "$current_dir/.specify" ]; then
+            echo "$current_dir"
+            return 0
+        fi
+        current_dir="$(dirname "$current_dir")"
+    done
+    
+    # Then check git if available
     if git rev-parse --show-toplevel >/dev/null 2>&1; then
         git rev-parse --show-toplevel
     else
diff --git a/scripts/bash/create-new-feature.sh b/scripts/bash/create-new-feature.sh
index 510f62046..1c47f5f72 100644
--- a/scripts/bash/create-new-feature.sh
+++ b/scripts/bash/create-new-feature.sh
@@ -59,21 +59,22 @@ find_repo_root() {
     return 1
 }
 
-# Resolve repository root. Prefer git information when available, but fall back
-# to searching for repository markers so the workflow still functions in repositories that
-# were initialised with --no-git.
+# Resolve repository root. Prioritize .specify directory over git information
+# to ensure specs/ is created in the correct location for multiproject setups.
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
-if git rev-parse --show-toplevel >/dev/null 2>&1; then
-    REPO_ROOT=$(git rev-parse --show-toplevel)
-    HAS_GIT=true
-else
-    REPO_ROOT="$(find_repo_root "$SCRIPT_DIR")"
-    if [ -z "$REPO_ROOT" ]; then
-        echo "Error: Could not determine repository root. Please run this script from within the repository." >&2
-        exit 1
+# First try to find .specify directory (highest priority)
+REPO_ROOT="$(find_repo_root "$SCRIPT_DIR")"
+if [ -n "$REPO_ROOT" ]; then
+    # Check if this is a git repository
+    if git rev-parse --show-toplevel >/dev/null 2>&1; then
+        HAS_GIT=true
+    else
+        HAS_GIT=false
     fi
-    HAS_GIT=false
+else
+    echo "Error: Could not determine repository root. Please run this script from within the repository." >&2
+    exit 1
 fi
 
 cd "$REPO_ROOT"
diff --git a/scripts/powershell/common.ps1 b/scripts/powershell/common.ps1
index b0be27354..dd1dfd652 100644
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -2,6 +2,17 @@
 # Common PowerShell functions analogous to common.sh
 
 function Get-RepoRoot {
+    # First check for .specify directory (highest priority)
+    $currentDir = Get-Location
+    while ($currentDir.Path -ne $currentDir.Drive.Root) {
+        $specifyPath = Join-Path $currentDir ".specify"
+        if (Test-Path $specifyPath -PathType Container) {
+            return $currentDir.Path
+        }
+        $currentDir = $currentDir.Parent
+    }
+    
+    # Then check git if available
     try {
         $result = git rev-parse --show-toplevel 2>$null
         if ($LASTEXITCODE -eq 0) {