diff --git a/esphome/build_gen/arduino8266.py b/esphome/build_gen/arduino8266.py
index 9dad8c8c41..1ed1404db3 100644
--- a/esphome/build_gen/arduino8266.py
+++ b/esphome/build_gen/arduino8266.py
@@ -456,7 +456,12 @@ def _flash_ld_name(board: str) -> str:
     """
     override = _pio_option("board_build.ldscript", "")
     if not override:
-        return ESP8266_LD_SCRIPTS[BOARDS[board][KEY_FLASH_SIZE]][1]
+        # The same per-board override the PlatformIO path pins (layout
+        # preservation, see boards.py)
+        board_data = BOARDS[board]
+        return board_data.get(
+            "ldscript", ESP8266_LD_SCRIPTS[board_data[KEY_FLASH_SIZE]][1]
+        )
     if Path(override).name != override:
         raise EsphomeError(
             f"board_build.ldscript must be a bare script name, got {override!r}"
@@ -893,6 +898,18 @@ def write_project(paths: InstalledPaths, ccache: str | None) -> bool:
         _LOGGER.warning(
             "build_unflags entries matched no build flag: %s", ", ".join(unmatched)
         )
+    # _LINKFLAGS stores -u and its operand as two tokens; unflagging the
+    # bare -u would strip all seven and leave the operands as ld "input
+    # files" with an error pointing nowhere near build_unflags
+    if plain := sorted(
+        u
+        for u in unflags
+        if u in _PLAIN_LINKER_FLAGS or u.startswith(_PLAIN_LINKER_PREFIXES)
+    ):
+        raise EsphomeError(
+            f"build_unflags cannot remove plain linker flag(s) "
+            f"{', '.join(plain)}; unflag the full -Wl, form or the symbol"
+        )
     cflags, cxxflags, asflags, link_flags = (
         [f for f in flags if f not in unflags]
         for flags in (cflags, cxxflags, asflags, _LINKFLAGS)
diff --git a/esphome/components/esp8266/__init__.py b/esphome/components/esp8266/__init__.py
index 5c8bef7fca..0c13625a64 100644
--- a/esphome/components/esp8266/__init__.py
+++ b/esphome/components/esp8266/__init__.py
@@ -409,8 +409,8 @@ async def to_code(config: ConfigType) -> None:
     )
 
     if config[CONF_BOARD] in BOARDS:
-        flash_size = BOARDS[config[CONF_BOARD]][KEY_FLASH_SIZE]
-        ld_scripts = ESP8266_LD_SCRIPTS[flash_size]
+        board_data = BOARDS[config[CONF_BOARD]]
+        ld_scripts = ESP8266_LD_SCRIPTS[board_data[KEY_FLASH_SIZE]]
 
         if ver <= cv.Version(2, 3, 0):
             # No ld script support
@@ -419,7 +419,9 @@ async def to_code(config: ConfigType) -> None:
             # Old ld script path
             ld_script = ld_scripts[0]
         else:
-            ld_script = ld_scripts[1]
+            # A per-board override preserves a layout the board shipped
+            # with (see d1_wroom_02 in boards.py)
+            ld_script = board_data.get("ldscript", ld_scripts[1])
 
         if ld_script is not None:
             cg.add_platformio_option("board_build.ldscript", ld_script)
diff --git a/esphome/components/esp8266/boards.py b/esphome/components/esp8266/boards.py
index 88fe74f59d..397de60e24 100644
--- a/esphome/components/esp8266/boards.py
+++ b/esphome/components/esp8266/boards.py
@@ -202,6 +202,11 @@ BOARDS = {
     "d1_wroom_02": {
         "name": "WeMos D1 ESP-WROOM-02",
         "flash_size": FLASH_SIZE_2_MB,
+        # This board joined BOARDS after shipping with the manifest default
+        # (64 KB filesystem region); the flash-size default (2m.ld) would
+        # move _FS_end and with it the preferences sector, wiping existing
+        # devices' flash-backed state on update.
+        "ldscript": "eagle.flash.2m64.ld",
     },
     "d1": {
         "name": "WEMOS D1 R1",
diff --git a/tests/unit_tests/build_gen/test_arduino8266.py b/tests/unit_tests/build_gen/test_arduino8266.py
index 94a0cb50db..358202e613 100644
--- a/tests/unit_tests/build_gen/test_arduino8266.py
+++ b/tests/unit_tests/build_gen/test_arduino8266.py
@@ -1447,12 +1447,29 @@ def test_flash_ld_name_honors_ldscript_override(tmp_path: Path) -> None:
         arduino8266._flash_ld_name("nodemcuv2")
 
 
-def test_write_project_quotes_spaced_ldscript_override(tmp_path: Path) -> None:
-    """An overridden script name re-quotes on the link line like every other
-    user token (a space would otherwise split into two argv elements)."""
+def test_unflagging_a_plain_linker_flag_raises(tmp_path: Path) -> None:
+    """build_unflags: -u would strip all seven -u tokens and leave the
+    operands as ld input files; refuse by name instead."""
+    paths = _make_framework(tmp_path)
+    _set_flags()
+    CORE.build_unflags = {"-u _printf_float"}
+    with pytest.raises(EsphomeError, match="cannot remove plain linker"):
+        _write_ninja(paths)
+
+
+def test_d1_wroom_02_keeps_its_shipped_flash_layout() -> None:
+    """The board joined BOARDS late; the flash-size default (2m.ld) would
+    move _FS_end and the preferences sector on existing devices."""
+    assert arduino8266._flash_ld_name("d1_wroom_02") == "eagle.flash.2m64.ld"
+    assert arduino8266._flash_ld_name("nodemcuv2") == "eagle.flash.4m.ld"
+
+
+def test_write_project_rejects_spaced_ldscript_override(tmp_path: Path) -> None:
+    """A spaced override never reaches the link line: generate_ld_scripts
+    rejects the name first (the -T _shell_token quoting behind it is
+    defence-in-depth)."""
     CORE.platformio_options = {"board_build.ldscript": "my script.ld"}
     paths = _make_framework(tmp_path)
     _set_flags()
-    content = _write_ninja(paths)
-    assert "'my script.ld'" in content or '"my script.ld"' in content
-    assert "-T my script.ld" not in content
+    with pytest.raises(EsphomeError, match="Invalid flash linker script name"):
+        arduino8266.write_project(paths, None)