diff --git a/spacy/cli/_util.py b/spacy/cli/_util.py
index c959c9861..676a7c8d7 100644
--- a/spacy/cli/_util.py
+++ b/spacy/cli/_util.py
@@ -1,4 +1,4 @@
-from typing import Dict, Any, Union, List, Optional, Tuple, TYPE_CHECKING
+from typing import Dict, Any, Union, List, Optional, Tuple, Iterable, TYPE_CHECKING
 import sys
 import shutil
 from pathlib import Path
@@ -193,12 +193,15 @@ def validate_project_commands(config: Dict[str, Any]) -> None:
                 )
 
 
-def get_hash(data) -> str:
+def get_hash(data, exclude: Iterable[str] = tuple()) -> str:
     """Get the hash for a JSON-serializable object.
 
     data: The data to hash.
+    exclude (Iterable[str]): Top-level keys to exclude if data is a dict.
     RETURNS (str): The hash.
     """
+    if isinstance(data, dict):
+        data = {k: v for k, v in data.items() if k not in exclude}
     data_str = srsly.json_dumps(data, sort_keys=True).encode("utf8")
     return hashlib.md5(data_str).hexdigest()
 
diff --git a/spacy/cli/project/remote_storage.py b/spacy/cli/project/remote_storage.py
index e7e7cbbe8..7e2caa8d7 100644
--- a/spacy/cli/project/remote_storage.py
+++ b/spacy/cli/project/remote_storage.py
@@ -7,7 +7,8 @@ import tarfile
 from pathlib import Path
 
 from .._util import get_hash, get_checksum, download_file, ensure_pathy
-from ...util import make_tempdir
+from ...util import make_tempdir, get_minor_version
+from ... import about
 
 if TYPE_CHECKING:
     from pathy import Pathy  # noqa: F401
@@ -129,7 +130,9 @@ def get_command_hash(
     currently installed packages, whatever environment variables have been marked
     as relevant, and the command.
     """
-    hashes = [site_hash, env_hash] + [get_checksum(dep) for dep in sorted(deps)]
+    spacy_v = get_minor_version(about.__version__)
+    dep_checksums = [get_checksum(dep) for dep in sorted(deps)]
+    hashes = [spacy_v, site_hash, env_hash] + dep_checksums
     hashes.extend(cmd)
     creation_bytes = "".join(hashes).encode("utf8")
     return hashlib.md5(creation_bytes).hexdigest()
diff --git a/spacy/cli/project/run.py b/spacy/cli/project/run.py
index 69c49fba7..94d4371d0 100644
--- a/spacy/cli/project/run.py
+++ b/spacy/cli/project/run.py
@@ -4,8 +4,10 @@ from wasabi import msg
 import sys
 import srsly
 
+from ... import about
+from ...git_info import GIT_VERSION
 from ...util import working_dir, run_command, split_command, is_cwd, join_command
-from ...util import SimpleFrozenList
+from ...util import SimpleFrozenList, is_minor_version_match
 from .._util import PROJECT_FILE, PROJECT_LOCK, load_project_config, get_hash
 from .._util import get_checksum, project_cli, Arg, Opt, COMMAND
 
@@ -63,11 +65,11 @@ def project_run(
                 err_kwargs = {"exits": 1} if not dry else {}
                 msg.fail(err, err_help, **err_kwargs)
         with working_dir(project_dir) as current_dir:
+            msg.divider(subcommand)
             rerun = check_rerun(current_dir, cmd)
             if not rerun and not force:
                 msg.info(f"Skipping '{cmd['name']}': nothing changed")
             else:
-                msg.divider(subcommand)
                 run_commands(cmd["script"], dry=dry)
                 if not dry:
                     update_lockfile(current_dir, cmd)
@@ -171,12 +173,18 @@ def validate_subcommand(
         )
 
 
-def check_rerun(project_dir: Path, command: Dict[str, Any]) -> bool:
+def check_rerun(
+    project_dir: Path,
+    command: Dict[str, Any],
+    check_spacy_version: bool = True,
+    check_spacy_commit: bool = False,
+) -> bool:
     """Check if a command should be rerun because its settings or inputs/outputs
     changed.
 
     project_dir (Path): The current project directory.
     command (Dict[str, Any]): The command, as defined in the project.yml.
+    strict_version (bool):
     RETURNS (bool): Whether to re-run the command.
     """
     lock_path = project_dir / PROJECT_LOCK
@@ -189,10 +197,23 @@ def check_rerun(project_dir: Path, command: Dict[str, Any]) -> bool:
     # Always run commands with no outputs (otherwise they'd always be skipped)
     if not entry.get("outs", []):
         return True
+    # Always rerun if spaCy version or commit hash changed
+    spacy_v = entry.get("spacy_version")
+    commit = entry.get("spacy_git_version")
+    if check_spacy_version and not is_minor_version_match(spacy_v, about.__version__):
+        info = f"({spacy_v} in {PROJECT_LOCK}, {about.__version__} current)"
+        msg.info(f"Re-running '{command['name']}': spaCy minor version changed {info}")
+        return True
+    if check_spacy_commit and commit != GIT_VERSION:
+        info = f"({commit} in {PROJECT_LOCK}, {GIT_VERSION} current)"
+        msg.info(f"Re-running '{command['name']}': spaCy commit changed {info}")
+        return True
     # If the entry in the lockfile matches the lockfile entry that would be
     # generated from the current command, we don't rerun because it means that
     # all inputs/outputs, hashes and scripts are the same and nothing changed
-    return get_hash(get_lock_entry(project_dir, command)) != get_hash(entry)
+    lock_entry = get_lock_entry(project_dir, command)
+    exclude = ["spacy_version", "spacy_git_version"]
+    return get_hash(lock_entry, exclude=exclude) != get_hash(entry, exclude=exclude)
 
 
 def update_lockfile(project_dir: Path, command: Dict[str, Any]) -> None:
@@ -231,6 +252,8 @@ def get_lock_entry(project_dir: Path, command: Dict[str, Any]) -> Dict[str, Any]
         "script": command["script"],
         "deps": deps,
         "outs": [*outs, *outs_nc],
+        "spacy_version": about.__version__,
+        "spacy_git_version": GIT_VERSION,
     }
 
 
diff --git a/spacy/tests/test_misc.py b/spacy/tests/test_misc.py
index bdf54ad6a..b9a0a9d05 100644
--- a/spacy/tests/test_misc.py
+++ b/spacy/tests/test_misc.py
@@ -149,6 +149,21 @@ def test_is_unconstrained_version(constraint, expected):
     assert util.is_unconstrained_version(constraint) is expected
 
 
+@pytest.mark.parametrize(
+    "a1,a2,b1,b2,is_match",
+    [
+        ("3.0.0", "3.0", "3.0.1", "3.0", True),
+        ("3.1.0", "3.1", "3.2.1", "3.2", False),
+        ("xxx", None, "1.2.3.dev0", "1.2", False),
+    ],
+)
+def test_minor_version(a1, a2, b1, b2, is_match):
+    assert util.get_minor_version(a1) == a2
+    assert util.get_minor_version(b1) == b2
+    assert util.is_minor_version_match(a1, b1) is is_match
+    assert util.is_minor_version_match(a2, b2) is is_match
+
+
 @pytest.mark.parametrize(
     "dot_notation,expected",
     [
diff --git a/spacy/util.py b/spacy/util.py
index 4d68e829c..4b2cb018a 100644
--- a/spacy/util.py
+++ b/spacy/util.py
@@ -584,6 +584,33 @@ def get_base_version(version: str) -> str:
     return Version(version).base_version
 
 
+def get_minor_version(version: str) -> Optional[str]:
+    """Get the major + minor version (without patch or prerelease identifiers).
+
+    version (str): The version.
+    RETURNS (str): The major + minor version or None if version is invalid.
+    """
+    try:
+        v = Version(version)
+    except (TypeError, InvalidVersion):
+        return None
+    return f"{v.major}.{v.minor}"
+
+
+def is_minor_version_match(version_a: str, version_b: str) -> bool:
+    """Compare two versions and check if they match in major and minor, without
+    patch or prerelease identifiers. Used internally for compatibility checks
+    that should be insensitive to patch releases.
+
+    version_a (str): The first version
+    version_b (str): The second version.
+    RETURNS (bool): Whether the versions match.
+    """
+    a = get_minor_version(version_a)
+    b = get_minor_version(version_b)
+    return a is not None and b is not None and a == b
+
+
 def load_meta(path: Union[str, Path]) -> Dict[str, Any]:
     """Load a model meta.json from a path and validate its contents.