diff --git a/ports/zephyr-cp/cptools/build_circuitpython.py b/ports/zephyr-cp/cptools/build_circuitpython.py
index 8594c245c81..c2a36eac8b3 100644
--- a/ports/zephyr-cp/cptools/build_circuitpython.py
+++ b/ports/zephyr-cp/cptools/build_circuitpython.py
@@ -632,6 +632,17 @@ async def build_circuitpython():  # noqa: C901
             logger.warning(
                 f"autogen_board_info.toml is missing or out of date. Please run `make BOARD={board}` locally and commit {autogen_board_info_fn}."
             )
+            # Also as an annotation, so it shows on the run and next to the file in the
+            # pull request rather than in one board log out of 29. The board builds once
+            # per language, so only the first build of it says anything.
+            reported = builddir / "autogen_board_info.reported"
+            if not reported.exists():
+                reported.touch()
+                print(
+                    f"::warning file={autogen_board_info_fn.relative_to(srcdir)}::"
+                    f"out of date, run `make BOARD={board}` and commit it",
+                    flush=True,
+                )
     autogen_modules.add(tomlkit.comment("extmod modules shared with MicroPython"))
     for extmod_module in EXTMOD_MODULES:
         enabled = extmod_module in enabled_modules
diff --git a/tools/ci_set_matrix.py b/tools/ci_set_matrix.py
index 26d3bed4ebc..4eef0060af5 100755
--- a/tools/ci_set_matrix.py
+++ b/tools/ci_set_matrix.py
@@ -28,6 +28,7 @@
 import json
 import pathlib
 import subprocess
+import tomllib
 from concurrent.futures import ThreadPoolExecutor
 
 tools_dir = pathlib.Path(__file__).resolve().parent
@@ -76,6 +77,35 @@
 # (this port has none), documentation or the unix test suite.
 PATTERN_ZEPHYR_TESTS_IGNORE = re.compile(r"^(?:docs|frozen|locale|tests)/|^ports/(?!zephyr-cp/)")
 
+# Zephyr boards don't use make, so their module tables can't be computed here. Each
+# board's build writes autogen_board_info.toml next to its circuitpython.toml and that
+# file is committed; a board whose table is missing, unreadable or doesn't name a
+# module is built.
+ZEPHYR_BOARDS = tools_dir.parent / "ports" / "zephyr-cp" / "boards"
+zephyr_modules = None
+
+
+def load_zephyr_modules():
+    modules = {}
+    for board_info in ZEPHYR_BOARDS.glob("*/*/autogen_board_info.toml"):
+        board = f"{board_info.parent.parent.name}_{board_info.parent.name}"
+        try:
+            with board_info.open("rb") as f:
+                modules[board] = tomllib.load(f)["modules"]
+        except Exception as e:  # noqa: BLE001 -- whatever went wrong, the board gets built
+            print(f"  {board}: unusable module table ({e})")
+    return modules
+
+
+def zephyr_board_has_module(board, module):
+    """What the board's committed module table says. An unknown board or module counts
+    as yes, so the board gets built."""
+    global zephyr_modules
+    if zephyr_modules is None:
+        zephyr_modules = load_zephyr_modules()
+    return board not in zephyr_modules or zephyr_modules[board].get(module, True)
+
+
 PATTERN_WINDOWS = {
     ".github/",
     "extmod/",
@@ -210,9 +240,16 @@ def get_settings(board):
                 # the logic to build all boards breaks.
                 boards = set(port_to_board[port] if port else all_board_ids)
 
-                # Zephyr boards don't use make, so build them and don't compute their settings.
-                for board in port_to_board["zephyr-cp"]:
-                    if board in boards:
+                # Zephyr boards don't use make, so decide them here from their committed
+                # module table and leave them out of the settings computation below.
+                module = module_matches.group(2) if module_matches else None
+                for board in list(boards):  # a copy, boards shrinks below
+                    if board_to_port[board] != "zephyr-cp":
+                        continue
+                    boards.remove(board)
+                    if file.startswith("frozen"):
+                        continue  # the port has no frozen modules
+                    if module is None or zephyr_board_has_module(board, module):
                         boards_to_build.add(board)
 
                 for board in boards_to_build: