diff --git a/ENVIRONMENT_VARIABLES.md b/ENVIRONMENT_VARIABLES.md
index 6f53f8d2..6bc1efa0 100644
--- a/ENVIRONMENT_VARIABLES.md
+++ b/ENVIRONMENT_VARIABLES.md
@@ -19,4 +19,5 @@ name | default | description
 `GOENV_AUTO_INSTALL_FLAGS` | | (Note: only works if `GOENV_AUTO_INSTALL` is set to 1) Appends flags to the auto install command (see `goenv install --help` for all available flags)
 `GOENV_RC_FILE` | `$HOME/.goenvrc` | If `GOENV_RC_FILE` is set, it will be modified accordingly.
 `GOENV_PATH_ORDER` | | If `GOENV_PATH_ORDER` is set to `front`, `$GOENV_ROOT/shims` will be prepended to the existing `PATH`.Set `GOENV_PATH_ORDER` to a configuration file named by `GOENV_RC_FILE`(e.g. `~/.goenvrc`), for example `GOENV_PATH_ORDER=front` in `~/.goenvrc`.
+`GOENV_DISABLE_PATH_WARNING` | `0` | Disables the warning about system Go taking precedence over goenv when shims are at the end of PATH. Set to `1` to disable the warning.
 `GOENV_AUTOMATICALLY_DETECT_VERSION` | `0` | If set to `1`, goenv will automatically update `GOROOT` and `GOPATH` when you change directories. This enables automatic version switching based on local `.go-version` files without needing to reload your shell configuration. **Note:** This feature adds a hook that runs on every directory change, which may have a slight performance impact.
diff --git a/HOW_IT_WORKS.md b/HOW_IT_WORKS.md
index cd3895b9..bfc95182 100644
--- a/HOW_IT_WORKS.md
+++ b/HOW_IT_WORKS.md
@@ -22,21 +22,28 @@ then `/bin`.
 
 ## Understanding Shims
 
-goenv works by inserting a directory of _shims_ at the end of your
-`PATH`, so if you have `go` in `/usr/bin` it will be found first:
+By default, goenv works by inserting a directory of _shims_ at the end of your
+`PATH`. This means if you have `go` in `/usr/bin`, it will be found first:
 
     /usr/local/bin:/usr/bin:/bin:~/.goenv/shims
 
+**Important:** If you have a system Go installation, you need to configure goenv
+to put shims at the front of your PATH. Add `export GOENV_PATH_ORDER=front` to
+your `~/.goenvrc` file (or your shell profile). This ensures goenv's shims take
+precedence:
+
+    ~/.goenv/shims:/usr/local/bin:/usr/bin:/bin
+
 Through a process called _rehashing_, goenv maintains shims in that
 directory to match every `go` command across every installed version
 of Go.
 
 Shims are lightweight executables that simply pass your command along
-to goenv. So with goenv installed, when you run `go` your
+to goenv. So with goenv properly configured, when you run `go` your
 operating system will do the following:
 
 * Search your `PATH` for an executable file named `go`
-* Find the goenv shim named `go` at the beginning of your `PATH`
+* Find the goenv shim named `go` at the beginning of your `PATH` (if `GOENV_PATH_ORDER=front`)
 * Run the shim named `go`, which in turn passes the command along to
   goenv
 
diff --git a/libexec/goenv-init b/libexec/goenv-init
index 872356d5..49ebe90f 100755
--- a/libexec/goenv-init
+++ b/libexec/goenv-init
@@ -86,23 +86,42 @@ mkdir -p "${GOENV_ROOT}/"{shims,versions}
 
 case "$shell" in
 fish)
-  cat <<EOL
-set -gx GOENV_SHELL ${shell}
-set -gx GOENV_ROOT ${GOENV_ROOT}
-if test -z \$GOENV_RC_FILE
-  set GOENV_RC_FILE \$HOME/.goenvrc
+  cat <<'EOL'
+set -gx GOENV_SHELL fish
+EOL
+  echo "set -gx GOENV_ROOT ${GOENV_ROOT}"
+  cat <<'EOL'
+if test -z $GOENV_RC_FILE
+  set GOENV_RC_FILE $HOME/.goenvrc
 end
-if test -e \$GOENV_RC_FILE
-  source \$GOENV_RC_FILE
+if test -e $GOENV_RC_FILE
+  source $GOENV_RC_FILE
 end
-if not contains \$GOENV_ROOT/shims \$PATH
-  if test "\$GOENV_PATH_ORDER" = "front"
-    set -gx PATH \$GOENV_ROOT/shims \$PATH
+if not contains $GOENV_ROOT/shims $PATH
+  if test "$GOENV_PATH_ORDER" = "front"
+    set -gx PATH $GOENV_ROOT/shims $PATH
   else
-    set -gx PATH \$PATH \$GOENV_ROOT/shims
+    set -gx PATH $PATH $GOENV_ROOT/shims
   end
 end
 EOL
+
+  # Add PATH collision warning unless explicitly disabled
+  if [ "${GOENV_DISABLE_PATH_WARNING:-0}" != "1" ]; then
+    cat <<'EOL'
+if test "$GOENV_PATH_ORDER" != "front"
+  set -l system_go_path (command -v go 2>/dev/null)
+  if test -n "$system_go_path"; and not string match -q "$GOENV_ROOT*" $system_go_path
+    echo "goenv: WARNING: System 'go' found at $system_go_path" >&2
+    echo "goenv: Since your shims are at the end of PATH, system 'go' will be used instead of goenv-managed versions." >&2
+    echo "goenv: To fix this, add the following to your $GOENV_RC_FILE:" >&2
+    echo "goenv:     set -gx GOENV_PATH_ORDER front" >&2
+    echo "goenv: Or run: echo 'set -gx GOENV_PATH_ORDER front' >> $GOENV_RC_FILE" >&2
+    echo "" >&2
+  end
+end
+EOL
+  fi
   ;;
 *)
   cat <<EOL
@@ -122,6 +141,29 @@ if [ "\${PATH#*\$GOENV_ROOT/shims}" = "\${PATH}" ]; then
   fi
 fi
 EOL
+
+  # Add PATH collision warning unless explicitly disabled
+  if [ "${GOENV_DISABLE_PATH_WARNING:-0}" != "1" ]; then
+    cat <<'EOL'
+if [ "${GOENV_PATH_ORDER:-}" != "front" ]; then
+  system_go_path="$(command -v go 2>/dev/null || true)"
+  if [ -n "$system_go_path" ]; then
+    case "$system_go_path" in
+      ${GOENV_ROOT}/*)
+        ;;
+      *)
+        echo "goenv: WARNING: System 'go' found at $system_go_path" >&2
+        echo "goenv: Since your shims are at the end of PATH, system 'go' will be used instead of goenv-managed versions." >&2
+        echo "goenv: To fix this, add the following to your ${GOENV_RC_FILE}:" >&2
+        echo "goenv:     export GOENV_PATH_ORDER=front" >&2
+        echo "goenv: Or run: echo 'export GOENV_PATH_ORDER=front' >> ${GOENV_RC_FILE}" >&2
+        echo "" >&2
+        ;;
+    esac
+  fi
+fi
+EOL
+  fi
   ;;
 esac
 
diff --git a/test/goenv-init.bats b/test/goenv-init.bats
index f89c3030..8faf30ec 100644
--- a/test/goenv-init.bats
+++ b/test/goenv-init.bats
@@ -377,3 +377,52 @@ OUT
   assert [ -n "$(echo "$output" | grep "__goenv_auto_detect_version")" ]
   assert [ -n "$(echo "$output" | grep "on-variable PWD")" ]
 }
+
+@test "includes PATH collision warning when system go exists and GOENV_PATH_ORDER is not front for bash" {
+  # Create a fake go binary in PATH
+  create_executable "${GOENV_TEST_DIR}/bin" "go"
+  
+  unset GOENV_DISABLE_PATH_WARNING
+  run goenv-init - bash
+  
+  assert_success
+  assert_line 'if [ "${GOENV_PATH_ORDER:-}" != "front" ]; then'
+  assert [ -n "$(echo "$output" | grep 'WARNING: System.*go.*found')" ]
+}
+
+@test "does not include PATH collision warning when GOENV_DISABLE_PATH_WARNING is set to 1" {
+  create_executable "${GOENV_TEST_DIR}/bin" "go"
+  
+  GOENV_DISABLE_PATH_WARNING=1 run goenv-init - bash
+  
+  assert_success
+  refute_line '  system_go_path="$(command -v go 2>/dev/null || true)"'
+}
+
+@test "warning executes and shows message when system go exists and GOENV_PATH_ORDER not set" {
+  # Create a fake go binary
+  create_executable "${GOENV_TEST_DIR}/bin" "go"
+  
+  # Don't disable the warning for this test
+  unset GOENV_DISABLE_PATH_WARNING
+  unset GOENV_PATH_ORDER
+  
+  # Eval the init output and capture stderr
+  run bash -c 'eval "$(GOENV_DISABLE_PATH_WARNING=0 goenv-init - bash 2>&1)" 2>&1'
+  
+  assert_success
+  assert [ -n "$(echo "$output" | grep 'WARNING: System.*go.*found')" ]
+  assert [ -n "$(echo "$output" | grep 'GOENV_PATH_ORDER=front')" ]
+}
+
+@test "warning does not execute when GOENV_PATH_ORDER is set to front" {
+  create_executable "${GOENV_TEST_DIR}/bin" "go"
+  
+  unset GOENV_DISABLE_PATH_WARNING
+  export GOENV_PATH_ORDER=front
+  
+  run bash -c 'eval "$(GOENV_DISABLE_PATH_WARNING=0 goenv-init - bash 2>&1)" 2>&1'
+  
+  assert_success
+  assert [ -z "$(echo "$output" | grep 'WARNING')" ]
+}
diff --git a/test/test_helper.bash b/test/test_helper.bash
index e723d1c2..9ed1594a 100644
--- a/test/test_helper.bash
+++ b/test/test_helper.bash
@@ -3,6 +3,9 @@ load ./test_assert_helpers
 unset GOENV_VERSION
 unset GOENV_DIR
 
+# Disable PATH warning in tests to avoid changing expected output
+export GOENV_DISABLE_PATH_WARNING=1
+
 # guard against executing this block twice due to bats internals
 if [ -z "$GOENV_TEST_DIR" ]; then
   GOENV_TEST_DIR="${BATS_TMPDIR}/goenv"