diff --git a/spacy/cli/__init__.py b/spacy/cli/__init__.py
index 0568b34de..eedd8961f 100644
--- a/spacy/cli/__init__.py
+++ b/spacy/cli/__init__.py
@@ -1,6 +1,6 @@
 from wasabi import msg
 
-from ._app import app, setup_cli  # noqa: F401
+from ._util import app, setup_cli  # noqa: F401
 
 # These are the actual functions, NOT the wrapped CLI commands. The CLI commands
 # are registered automatically and won't have to be imported here.
diff --git a/spacy/cli/_app.py b/spacy/cli/_app.py
deleted file mode 100644
index e970c4dde..000000000
--- a/spacy/cli/_app.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import typer
-from typer.main import get_command
-
-
-COMMAND = "python -m spacy"
-NAME = "spacy"
-HELP = """spaCy Command-line Interface
-
-DOCS: https://spacy.io/api/cli
-"""
-PROJECT_HELP = f"""Command-line interface for spaCy projects and working with
-project templates. You'd typically start by cloning a project template to a local
-directory and fetching its assets like datasets etc. See the project's
-project.yml for the available commands.
-"""
-
-
-app = typer.Typer(name=NAME, help=HELP)
-project_cli = typer.Typer(name="project", help=PROJECT_HELP, no_args_is_help=True)
-app.add_typer(project_cli)
-
-# Wrappers for Typer's annotations. Initially created to set defaults and to
-# keep the names short, but not needed at the moment.
-Arg = typer.Argument
-Opt = typer.Option
-
-
-def setup_cli() -> None:
-    # Ensure that the help messages always display the correct prompt
-    command = get_command(app)
-    command(prog_name=COMMAND)
diff --git a/spacy/cli/project/util.py b/spacy/cli/_util.py
similarity index 57%
rename from spacy/cli/project/util.py
rename to spacy/cli/_util.py
index 1111ddc2d..4289df856 100644
--- a/spacy/cli/project/util.py
+++ b/spacy/cli/_util.py
@@ -1,14 +1,76 @@
-from typing import Dict, Any, Union
+from typing import Dict, Any, Union, List
 from pathlib import Path
 from wasabi import msg
 import srsly
 import hashlib
+import typer
+from typer.main import get_command
 
-from ...schemas import ProjectConfigSchema, validate
+from ..schemas import ProjectConfigSchema, validate
 
 
 PROJECT_FILE = "project.yml"
 PROJECT_LOCK = "project.lock"
+COMMAND = "python -m spacy"
+NAME = "spacy"
+HELP = """spaCy Command-line Interface
+
+DOCS: https://spacy.io/api/cli
+"""
+PROJECT_HELP = f"""Command-line interface for spaCy projects and working with
+project templates. You'd typically start by cloning a project template to a local
+directory and fetching its assets like datasets etc. See the project's
+{PROJECT_FILE} for the available commands.
+"""
+
+# Wrappers for Typer's annotations. Initially created to set defaults and to
+# keep the names short, but not needed at the moment.
+Arg = typer.Argument
+Opt = typer.Option
+
+app = typer.Typer(name=NAME, help=HELP)
+project_cli = typer.Typer(name="project", help=PROJECT_HELP, no_args_is_help=True)
+app.add_typer(project_cli)
+
+
+def setup_cli() -> None:
+    # Ensure that the help messages always display the correct prompt
+    command = get_command(app)
+    command(prog_name=COMMAND)
+
+
+def parse_config_overrides(args: List[str]) -> Dict[str, Any]:
+    """Generate a dictionary of config overrides based on the extra arguments
+    provided on the CLI, e.g. --training.batch_size to override
+    "training.batch_size". Arguments without a "." are considered invalid,
+    since the config only allows top-level sections to exist.
+
+    args (List[str]): The extra arguments from the command line.
+    RETURNS (Dict[str, Any]): The parsed dict, keyed by nested config setting.
+    """
+    result = {}
+    while args:
+        opt = args.pop(0)
+        err = f"Invalid config override '{opt}'"
+        if opt.startswith("--"):  # new argument
+            opt = opt.replace("--", "")
+            if "." not in opt:
+                msg.fail(f"{err}: can't override top-level section", exits=1)
+            if not args or args[0].startswith("--"):  # flag with no value
+                value = True
+            else:
+                value = args.pop(0)
+            # Just like we do in the config, we're calling json.loads on the
+            # values. But since they come from the CLI, it'd b unintuitive to
+            # explicitly mark strings with escaped quotes. So we're working
+            # around that here by falling back to a string if parsing fails.
+            try:
+                result[opt] = srsly.json_loads(value)
+            except ValueError:
+                result[opt] = str(value)
+        else:
+            msg.fail(f"{err}: options need to start with --", exits=1)
+    return result
 
 
 def load_project_config(path: Path) -> Dict[str, Any]:
diff --git a/spacy/cli/convert.py b/spacy/cli/convert.py
index c26b5ee75..3c04ca15c 100644
--- a/spacy/cli/convert.py
+++ b/spacy/cli/convert.py
@@ -6,7 +6,7 @@ import srsly
 import re
 import sys
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from ..gold import docs_to_json
 from ..tokens import DocBin
 from ..gold.converters import iob2docs, conll_ner2docs, json2docs, conllu2docs
diff --git a/spacy/cli/debug_data.py b/spacy/cli/debug_data.py
index 712bc7914..df3236511 100644
--- a/spacy/cli/debug_data.py
+++ b/spacy/cli/debug_data.py
@@ -5,7 +5,7 @@ import sys
 import srsly
 from wasabi import Printer, MESSAGES
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from ..gold import Corpus, Example
 from ..syntax import nonproj
 from ..language import Language
diff --git a/spacy/cli/download.py b/spacy/cli/download.py
index f192cb196..cdbd7514a 100644
--- a/spacy/cli/download.py
+++ b/spacy/cli/download.py
@@ -4,7 +4,7 @@ import sys
 from wasabi import msg
 import typer
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from .. import about
 from ..util import is_package, get_base_version, run_command
 
diff --git a/spacy/cli/evaluate.py b/spacy/cli/evaluate.py
index a5d4a3661..3467204b9 100644
--- a/spacy/cli/evaluate.py
+++ b/spacy/cli/evaluate.py
@@ -8,7 +8,7 @@ from thinc.api import require_gpu, fix_random_seed
 
 from ..gold import Corpus
 from ..tokens import Doc
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from ..scorer import Scorer
 from .. import util
 from .. import displacy
diff --git a/spacy/cli/info.py b/spacy/cli/info.py
index 9f1ec3855..98a1efeb8 100644
--- a/spacy/cli/info.py
+++ b/spacy/cli/info.py
@@ -4,7 +4,7 @@ from pathlib import Path
 from wasabi import Printer
 import srsly
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from .. import util
 from .. import about
 
diff --git a/spacy/cli/init_model.py b/spacy/cli/init_model.py
index 5cfde43e0..e8c17ae33 100644
--- a/spacy/cli/init_model.py
+++ b/spacy/cli/init_model.py
@@ -12,7 +12,7 @@ import srsly
 import warnings
 from wasabi import Printer
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from ..vectors import Vectors
 from ..errors import Errors, Warnings
 from ..language import Language
diff --git a/spacy/cli/package.py b/spacy/cli/package.py
index dbc485848..74f9b0c96 100644
--- a/spacy/cli/package.py
+++ b/spacy/cli/package.py
@@ -5,7 +5,7 @@ from wasabi import Printer, get_raw_input
 import srsly
 import sys
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from ..schemas import validate, ModelMetaSchema
 from .. import util
 from .. import about
diff --git a/spacy/cli/pretrain.py b/spacy/cli/pretrain.py
index 58e82028b..d1fa71fd7 100644
--- a/spacy/cli/pretrain.py
+++ b/spacy/cli/pretrain.py
@@ -12,7 +12,7 @@ from wasabi import msg
 import srsly
 from functools import partial
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from ..errors import Errors
 from ..ml.models.multi_task import build_cloze_multi_task_model
 from ..ml.models.multi_task import build_cloze_characters_multi_task_model
diff --git a/spacy/cli/profile.py b/spacy/cli/profile.py
index 3dc9f1027..2faf002d0 100644
--- a/spacy/cli/profile.py
+++ b/spacy/cli/profile.py
@@ -8,7 +8,7 @@ import sys
 import itertools
 from wasabi import msg, Printer
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt
 from ..language import Language
 from ..util import load_model
 
diff --git a/spacy/cli/project/assets.py b/spacy/cli/project/assets.py
index 2270574ab..2b7dbaf66 100644
--- a/spacy/cli/project/assets.py
+++ b/spacy/cli/project/assets.py
@@ -7,8 +7,7 @@ import re
 import shutil
 
 from ...util import ensure_path, working_dir
-from .._app import project_cli, Arg
-from .util import PROJECT_FILE, load_project_config, get_checksum
+from .._util import project_cli, Arg, PROJECT_FILE, load_project_config, get_checksum
 
 
 # TODO: find a solution for caches
diff --git a/spacy/cli/project/clone.py b/spacy/cli/project/clone.py
index 6ce2d309e..bb9ba74cb 100644
--- a/spacy/cli/project/clone.py
+++ b/spacy/cli/project/clone.py
@@ -7,8 +7,7 @@ import re
 
 from ... import about
 from ...util import ensure_path, run_command, make_tempdir
-from .._app import project_cli, Arg, Opt, COMMAND
-from .util import PROJECT_FILE
+from .._util import project_cli, Arg, Opt, COMMAND, PROJECT_FILE
 
 
 @project_cli.command("clone")
diff --git a/spacy/cli/project/dvc.py b/spacy/cli/project/dvc.py
index c29618820..7386339d9 100644
--- a/spacy/cli/project/dvc.py
+++ b/spacy/cli/project/dvc.py
@@ -5,8 +5,8 @@ import subprocess
 from pathlib import Path
 from wasabi import msg
 
-from .util import PROJECT_FILE, load_project_config, get_hash
-from .._app import project_cli, Arg, Opt, NAME, COMMAND
+from .._util import PROJECT_FILE, load_project_config, get_hash, project_cli
+from .._util import Arg, Opt, NAME, COMMAND
 from ...util import working_dir, split_command, join_command, run_command
 
 
diff --git a/spacy/cli/project/run.py b/spacy/cli/project/run.py
index a8cc58c01..5c66095aa 100644
--- a/spacy/cli/project/run.py
+++ b/spacy/cli/project/run.py
@@ -5,9 +5,8 @@ import sys
 import srsly
 
 from ...util import working_dir, run_command, split_command, is_cwd, join_command
-from .._app import project_cli, Arg, Opt, COMMAND
-from .util import PROJECT_FILE, PROJECT_LOCK, load_project_config, get_hash
-from .util import get_checksum
+from .._util import PROJECT_FILE, PROJECT_LOCK, load_project_config, get_hash
+from .._util import get_checksum, project_cli, Arg, Opt, COMMAND
 
 
 @project_cli.command("run")
diff --git a/spacy/cli/train.py b/spacy/cli/train.py
index 45520978b..32d1a456e 100644
--- a/spacy/cli/train.py
+++ b/spacy/cli/train.py
@@ -1,4 +1,4 @@
-from typing import Optional, Dict
+from typing import Optional, Dict, Any
 from timeit import default_timer as timer
 import srsly
 import tqdm
@@ -8,8 +8,9 @@ import thinc
 import thinc.schedules
 from thinc.api import use_pytorch_for_gpu_memory, require_gpu, fix_random_seed
 import random
+import typer
 
-from ._app import app, Arg, Opt
+from ._util import app, Arg, Opt, parse_config_overrides
 from ..gold import Corpus, Example
 from ..lookups import Lookups
 from .. import util
@@ -24,9 +25,12 @@ from ..ml import models  # noqa: F401
 registry = util.registry
 
 
-@app.command("train")
+@app.command(
+    "train", context_settings={"allow_extra_args": True, "ignore_unknown_options": True}
+)
 def train_cli(
     # fmt: off
+    ctx: typer.Context,  # This is only used to read additional arguments
     train_path: Path = Arg(..., help="Location of training data", exists=True),
     dev_path: Path = Arg(..., help="Location of development data", exists=True),
     config_path: Path = Arg(..., help="Path to config file", exists=True),
@@ -36,17 +40,36 @@ def train_cli(
     # fmt: on
 ):
     """
-    Train or update a spaCy model. Requires data to be formatted in spaCy's
-    JSON format. To convert data from other formats, use the `spacy convert`
-    command.
+    Train or update a spaCy model. Requires data in spaCy's binary format. To
+    convert data from other formats, use the `spacy convert` command. The
+    config file includes all settings and hyperparameters used during traing.
+    To override settings in the config, e.g. settings that point to local
+    paths or that you want to experiment with, you can override them as
+    command line options. For instance, --training.batch_size 128 overrides
+    the value of "batch_size" in the block "[training]". The --code argument
+    lets you pass in a Python file that's imported before training. It can be
+    used to register custom functions and architectures that can then be
+    referenced in the config.
     """
     util.set_env_log(verbose)
-    verify_cli_args(**locals())
-    try:
-        util.import_file("python_code", code_path)
-    except Exception as e:
-        msg.fail(f"Couldn't load Python code: {code_path}", e, exits=1)
-    train(config_path, {"train": train_path, "dev": dev_path}, output_path=output_path)
+    verify_cli_args(
+        train_path=train_path,
+        dev_path=dev_path,
+        config_path=config_path,
+        code_path=code_path,
+    )
+    overrides = parse_config_overrides(ctx.args)
+    if code_path is not None:
+        try:
+            util.import_file("python_code", code_path)
+        except Exception as e:
+            msg.fail(f"Couldn't load Python code: {code_path}", e, exits=1)
+    train(
+        config_path,
+        {"train": train_path, "dev": dev_path},
+        output_path=output_path,
+        config_overrides=overrides,
+    )
 
 
 def train(
@@ -54,7 +77,7 @@ def train(
     data_paths: Dict[str, Path],
     raw_text: Optional[Path] = None,
     output_path: Optional[Path] = None,
-    weights_data: Optional[bytes] = None,
+    config_overrides: Dict[str, Any] = {},
 ) -> None:
     msg.info(f"Loading config from: {config_path}")
     # Read the config first without creating objects, to get to the original nlp_config
@@ -469,7 +492,6 @@ def verify_cli_args(
     config_path: Path,
     output_path: Optional[Path] = None,
     code_path: Optional[Path] = None,
-    verbose: bool = False,
 ):
     # Make sure all files and paths exists if they are needed
     if not config_path or not config_path.exists():
diff --git a/spacy/cli/validate.py b/spacy/cli/validate.py
index 4271817f1..0580d34c5 100644
--- a/spacy/cli/validate.py
+++ b/spacy/cli/validate.py
@@ -4,7 +4,7 @@ import sys
 import requests
 from wasabi import msg, Printer
 
-from ._app import app
+from ._util import app
 from .. import about
 from ..util import get_package_version, get_installed_models, get_base_version
 from ..util import get_package_path, get_model_meta, is_compatible_version
diff --git a/spacy/tests/test_projects.py b/spacy/tests/test_projects.py
index c3477f463..65ac5739d 100644
--- a/spacy/tests/test_projects.py
+++ b/spacy/tests/test_projects.py
@@ -1,5 +1,5 @@
 import pytest
-from spacy.cli.project.util import validate_project_commands
+from spacy.cli._util import validate_project_commands
 from spacy.schemas import ProjectConfigSchema, validate