diff --git a/src/batdetect2/api_v2.py b/src/batdetect2/api_v2.py
index 10e5169..bd226b8 100644
--- a/src/batdetect2/api_v2.py
+++ b/src/batdetect2/api_v2.py
@@ -8,7 +8,6 @@ from soundevent.audio.files import get_audio_files
 
 from batdetect2.audio import AudioConfig, AudioLoader, build_audio_loader
 from batdetect2.config import BatDetect2Config
-from batdetect2.core import merge_configs
 from batdetect2.data import Dataset, load_dataset_from_config
 from batdetect2.evaluate import (
     DEFAULT_EVAL_DIR,
@@ -47,7 +46,7 @@ from batdetect2.postprocess import (
     build_postprocessor,
 )
 from batdetect2.preprocess import PreprocessorProtocol, build_preprocessor
-from batdetect2.targets import TargetProtocol, build_targets
+from batdetect2.targets import TargetConfig, TargetProtocol, build_targets
 from batdetect2.train import (
     DEFAULT_CHECKPOINT_DIR,
     TrainingConfig,
@@ -110,6 +109,7 @@ class BatDetect2API:
         num_epochs: int | None = None,
         run_name: str | None = None,
         seed: int | None = None,
+        model_config: ModelConfig | None = None,
         audio_config: AudioConfig | None = None,
         train_config: TrainingConfig | None = None,
     ):
@@ -118,7 +118,7 @@ class BatDetect2API:
             val_annotations=val_annotations,
             model=self.model,
             targets=self.targets,
-            model_config=self.model_config,
+            model_config=model_config or self.model_config,
             audio_loader=self.audio_loader,
             preprocessor=self.preprocessor,
             train_workers=train_workers,
@@ -149,6 +149,7 @@ class BatDetect2API:
         num_epochs: int | None = None,
         run_name: str | None = None,
         seed: int | None = None,
+        model_config: ModelConfig | None = None,
         audio_config: AudioConfig | None = None,
         train_config: TrainingConfig | None = None,
     ) -> "BatDetect2API":
@@ -161,7 +162,7 @@ class BatDetect2API:
             val_annotations=val_annotations,
             model=self.model,
             targets=self.targets,
-            model_config=self.model_config,
+            model_config=model_config or self.model_config,
             preprocessor=self.preprocessor,
             audio_loader=self.audio_loader,
             train_workers=train_workers,
@@ -499,76 +500,77 @@ class BatDetect2API:
     def from_checkpoint(
         cls,
         path: data.PathLike,
-        config: BatDetect2Config | None = None,
-        targets: TargetProtocol | None = None,
+        targets_config: TargetConfig | None = None,
+        audio_config: AudioConfig | None = None,
+        train_config: TrainingConfig | None = None,
+        evaluation_config: EvaluationConfig | None = None,
+        inference_config: InferenceConfig | None = None,
+        outputs_config: OutputsConfig | None = None,
     ) -> "BatDetect2API":
-        from batdetect2.audio import AudioConfig
-
         model, model_config = load_model_from_checkpoint(path)
 
-        # Reconstruct a full BatDetect2Config from the checkpoint's
-        # ModelConfig, then overlay any caller-supplied overrides.
-        base = BatDetect2Config(
-            model=model_config,
-            audio=AudioConfig(samplerate=model_config.samplerate),
+        audio_config = audio_config or AudioConfig(
+            samplerate=model_config.samplerate,
         )
-        config = merge_configs(base, config) if config else base
+        train_config = train_config or TrainingConfig()
+        evaluation_config = evaluation_config or EvaluationConfig()
+        inference_config = inference_config or InferenceConfig()
+        outputs_config = outputs_config or OutputsConfig()
 
-        if targets is None:
-            targets = build_targets(config=config.model.targets)
-        else:
-            target_config = getattr(targets, "config", None)
-            if target_config is not None:
-                config.model.targets = target_config
-
-        audio_loader = build_audio_loader(config=config.audio)
-
-        preprocessor = build_preprocessor(
-            input_samplerate=audio_loader.samplerate,
-            config=config.model.preprocess,
-        )
-
-        postprocessor = build_postprocessor(
-            preprocessor,
-            config=config.model.postprocess,
-        )
-
-        formatter = build_output_formatter(
-            targets,
-            config=config.outputs.format,
-        )
-        output_transform = build_output_transform(
-            config=config.outputs.transform,
-            targets=targets,
-        )
-
-        evaluator = build_evaluator(
-            config=config.evaluation,
-            targets=targets,
-            transform=output_transform,
-        )
-
-        targets_changed = targets is not None or (
-            config.model.targets.model_dump(mode="json")
-            != model_config.targets.model_dump(mode="json")
-        )
-        if targets_changed:
+        if (
+            targets_config is not None
+            and targets_config != model_config.targets
+        ):
+            targets = build_targets(config=targets_config)
             model = build_model_with_new_targets(
                 model=model,
                 targets=targets,
             )
+            model_config = model_config.model_copy(
+                update={"targets": targets_config}
+            )
+
+        targets = build_targets(config=model_config.targets)
+
+        audio_loader = build_audio_loader(config=audio_config)
+
+        preprocessor = build_preprocessor(
+            input_samplerate=audio_loader.samplerate,
+            config=model_config.preprocess,
+        )
+
+        postprocessor = build_postprocessor(
+            preprocessor,
+            config=model_config.postprocess,
+        )
+
+        formatter = build_output_formatter(
+            targets,
+            config=outputs_config.format,
+        )
+
+        output_transform = build_output_transform(
+            config=outputs_config.transform,
+            targets=targets,
+        )
+
+        evaluator = build_evaluator(
+            config=evaluation_config,
+            targets=targets,
+            transform=output_transform,
+        )
 
         model.preprocessor = preprocessor
         model.postprocessor = postprocessor
         model.targets = targets
 
         return cls(
-            model_config=config.model,
-            audio_config=config.audio,
-            train_config=config.train,
-            evaluation_config=config.evaluation,
-            inference_config=config.inference,
-            outputs_config=config.outputs,
+            model_config=model_config,
+            audio_config=audio_config,
+            train_config=train_config,
+            evaluation_config=evaluation_config,
+            inference_config=inference_config,
+            outputs_config=outputs_config,
             targets=targets,
             audio_loader=audio_loader,
             preprocessor=preprocessor,
diff --git a/src/batdetect2/cli/evaluate.py b/src/batdetect2/cli/evaluate.py
index f0d6517..9c76a33 100644
--- a/src/batdetect2/cli/evaluate.py
+++ b/src/batdetect2/cli/evaluate.py
@@ -12,9 +12,13 @@ DEFAULT_OUTPUT_DIR = Path("outputs") / "evaluation"
 
 
 @cli.command(name="evaluate")
-@click.argument("model-path", type=click.Path(exists=True))
+@click.argument("model_path", type=click.Path(exists=True))
 @click.argument("test_dataset", type=click.Path(exists=True))
-@click.option("--config", "config_path", type=click.Path())
+@click.option("--targets", "targets_config", type=click.Path(exists=True))
+@click.option("--audio-config", type=click.Path(exists=True))
+@click.option("--evaluation-config", type=click.Path(exists=True))
+@click.option("--inference-config", type=click.Path(exists=True))
+@click.option("--outputs-config", type=click.Path(exists=True))
 @click.option("--base-dir", type=click.Path(), default=Path.cwd())
 @click.option("--output-dir", type=click.Path(), default=DEFAULT_OUTPUT_DIR)
 @click.option("--experiment-name", type=str)
@@ -24,15 +28,23 @@ def evaluate_command(
     model_path: Path,
     test_dataset: Path,
     base_dir: Path,
-    config_path: Path | None,
+    targets_config: Path | None,
+    audio_config: Path | None,
+    evaluation_config: Path | None,
+    inference_config: Path | None,
+    outputs_config: Path | None,
     output_dir: Path = DEFAULT_OUTPUT_DIR,
     num_workers: int = 0,
     experiment_name: str | None = None,
     run_name: str | None = None,
 ):
     from batdetect2.api_v2 import BatDetect2API
-    from batdetect2.config import load_full_config
+    from batdetect2.audio import AudioConfig
     from batdetect2.data import load_dataset_from_config
+    from batdetect2.evaluate import load_evaluation_config
+    from batdetect2.inference import InferenceConfig
+    from batdetect2.outputs import OutputsConfig
+    from batdetect2.targets import load_target_config
 
     logger.info("Initiating evaluation process...")
 
@@ -46,11 +58,38 @@ def evaluate_command(
         num_annotations=len(test_annotations),
     )
 
-    config = None
-    if config_path is not None:
-        config = load_full_config(config_path)
+    target_conf = (
+        load_target_config(targets_config)
+        if targets_config is not None
+        else None
+    )
+    audio_conf = (
+        AudioConfig.load(audio_config) if audio_config is not None else None
+    )
+    eval_conf = (
+        load_evaluation_config(evaluation_config)
+        if evaluation_config is not None
+        else None
+    )
+    inference_conf = (
+        InferenceConfig.load(inference_config)
+        if inference_config is not None
+        else None
+    )
+    outputs_conf = (
+        OutputsConfig.load(outputs_config)
+        if outputs_config is not None
+        else None
+    )
 
-    api = BatDetect2API.from_checkpoint(model_path, config=config)
+    api = BatDetect2API.from_checkpoint(
+        model_path,
+        targets_config=target_conf,
+        audio_config=audio_conf,
+        evaluation_config=eval_conf,
+        inference_config=inference_conf,
+        outputs_config=outputs_conf,
+    )
 
     api.evaluate(
         test_annotations,
diff --git a/src/batdetect2/cli/train.py b/src/batdetect2/cli/train.py
index 8837ad8..b473a60 100644
--- a/src/batdetect2/cli/train.py
+++ b/src/batdetect2/cli/train.py
@@ -13,10 +13,14 @@ __all__ = ["train_command"]
 @click.option("--val-dataset", type=click.Path(exists=True))
 @click.option("--model", "model_path", type=click.Path(exists=True))
 @click.option("--targets", "targets_config", type=click.Path(exists=True))
+@click.option("--model-config", type=click.Path(exists=True))
+@click.option("--training-config", type=click.Path(exists=True))
+@click.option("--audio-config", type=click.Path(exists=True))
+@click.option("--evaluation-config", type=click.Path(exists=True))
+@click.option("--inference-config", type=click.Path(exists=True))
+@click.option("--outputs-config", type=click.Path(exists=True))
 @click.option("--ckpt-dir", type=click.Path(exists=True))
 @click.option("--log-dir", type=click.Path(exists=True))
-@click.option("--config", type=click.Path(exists=True))
-@click.option("--config-field", type=str)
 @click.option("--train-workers", type=int)
 @click.option("--val-workers", type=int)
 @click.option("--num-epochs", type=int)
@@ -29,9 +33,13 @@ def train_command(
     model_path: Path | None = None,
     ckpt_dir: Path | None = None,
     log_dir: Path | None = None,
-    config: Path | None = None,
     targets_config: Path | None = None,
-    config_field: str | None = None,
+    model_config: Path | None = None,
+    training_config: Path | None = None,
+    audio_config: Path | None = None,
+    evaluation_config: Path | None = None,
+    inference_config: Path | None = None,
+    outputs_config: Path | None = None,
     seed: int | None = None,
     num_epochs: int | None = None,
     train_workers: int = 0,
@@ -40,27 +48,56 @@ def train_command(
     run_name: str | None = None,
 ):
     from batdetect2.api_v2 import BatDetect2API
-    from batdetect2.config import (
-        BatDetect2Config,
-        load_full_config,
-    )
+    from batdetect2.audio import AudioConfig
+    from batdetect2.config import BatDetect2Config
     from batdetect2.data import load_dataset_from_config
+    from batdetect2.evaluate import load_evaluation_config
+    from batdetect2.inference import InferenceConfig
+    from batdetect2.models import ModelConfig
+    from batdetect2.outputs import OutputsConfig
     from batdetect2.targets import load_target_config
+    from batdetect2.train import load_train_config
 
     logger.info("Initiating training process...")
 
     logger.info("Loading configuration...")
-    conf = (
-        load_full_config(config, field=config_field)
-        if config is not None
-        else BatDetect2Config()
+    target_conf = (
+        load_target_config(targets_config)
+        if targets_config is not None
+        else None
+    )
+    model_conf = (
+        ModelConfig.load(model_config) if model_config is not None else None
+    )
+    train_conf = (
+        load_train_config(training_config)
+        if training_config is not None
+        else None
+    )
+    audio_conf = (
+        AudioConfig.load(audio_config) if audio_config is not None else None
+    )
+    eval_conf = (
+        load_evaluation_config(evaluation_config)
+        if evaluation_config is not None
+        else None
+    )
+    inference_conf = (
+        InferenceConfig.load(inference_config)
+        if inference_config is not None
+        else None
+    )
+    outputs_conf = (
+        OutputsConfig.load(outputs_config)
+        if outputs_config is not None
+        else None
     )
 
-    if targets_config is not None:
-        logger.info("Loading targets configuration...")
-        conf = conf.model_copy(
-            update=dict(targets=load_target_config(targets_config))
-        )
+    if target_conf is not None:
+        logger.info("Loaded targets configuration.")
+
+    if model_conf is not None and target_conf is not None:
+        model_conf = model_conf.model_copy(update={"targets": target_conf})
 
     logger.info("Loading training dataset...")
     train_annotations = load_dataset_from_config(train_dataset)
@@ -81,12 +118,40 @@ def train_command(
 
     logger.info("Configuration and data loaded. Starting training...")
 
+    if model_path is not None and model_conf is not None:
+        raise click.UsageError(
+            "--model-config cannot be used with --model. "
+            "Checkpoint model configuration is loaded from the checkpoint."
+        )
+
     if model_path is None:
+        conf = BatDetect2Config()
+        if model_conf is not None:
+            conf.model = model_conf
+        elif target_conf is not None:
+            conf.model = conf.model.model_copy(update={"targets": target_conf})
+
+        if train_conf is not None:
+            conf.train = train_conf
+        if audio_conf is not None:
+            conf.audio = audio_conf
+        if eval_conf is not None:
+            conf.evaluation = eval_conf
+        if inference_conf is not None:
+            conf.inference = inference_conf
+        if outputs_conf is not None:
+            conf.outputs = outputs_conf
+
         api = BatDetect2API.from_config(conf)
     else:
         api = BatDetect2API.from_checkpoint(
             model_path,
-            config=conf if config is not None else None,
+            targets_config=target_conf,
+            train_config=train_conf,
+            audio_config=audio_conf,
+            evaluation_config=eval_conf,
+            inference_config=inference_conf,
+            outputs_config=outputs_conf,
         )
 
     return api.train(
diff --git a/src/batdetect2/core/configs.py b/src/batdetect2/core/configs.py
index 118d366..49bb435 100644
--- a/src/batdetect2/core/configs.py
+++ b/src/batdetect2/core/configs.py
@@ -8,7 +8,6 @@ configuration data from files, with optional support for accessing nested
 configuration sections.
 """
 
-import sys
 from typing import Any, Type, TypeVar, overload
 
 import yaml
@@ -16,17 +15,14 @@ from deepmerge.merger import Merger
 from pydantic import BaseModel, ConfigDict, TypeAdapter
 from soundevent.data import PathLike
 
-if sys.version_info < (3, 11):
-    from typing_extensions import Self
-else:
-    from typing import Self
-
 __all__ = [
     "BaseConfig",
     "load_config",
     "merge_configs",
 ]
 
+C = TypeVar("C", bound="BaseConfig")
+
 
 class BaseConfig(BaseModel):
     """Base class for all configuration models in BatDetect2.
@@ -73,8 +69,8 @@ class BaseConfig(BaseModel):
         return cls.model_validate(yaml.safe_load(yaml_str))
 
     @classmethod
-    def load(cls: Self, path: PathLike, field: str | None = None) -> Self:
-        return load_config(path, schema=cls, field=field)  # type: ignore
+    def load(cls: Type[C], path: PathLike, field: str | None = None) -> C:
+        return load_config(path, schema=cls, field=field)
 
 
 T = TypeVar("T")
diff --git a/tests/test_api_v2/test_api_v2.py b/tests/test_api_v2/test_api_v2.py
index 4b3f71e..71a102a 100644
--- a/tests/test_api_v2/test_api_v2.py
+++ b/tests/test_api_v2/test_api_v2.py
@@ -201,7 +201,10 @@ def test_user_can_load_checkpoint_and_finetune(
     config.train.train_loader.batch_size = 1
     config.train.train_loader.augmentations.enabled = False
 
-    api = BatDetect2API.from_checkpoint(checkpoint_path, config=config)
+    api = BatDetect2API.from_checkpoint(
+        checkpoint_path,
+        train_config=config.train,
+    )
     finetune_dir = tmp_path / "finetuned"
 
     api.train(
@@ -234,13 +237,13 @@ def test_user_can_load_checkpoint_with_new_targets(
     source_model, _ = load_model_from_checkpoint(checkpoint_path)
     api = BatDetect2API.from_checkpoint(
         checkpoint_path,
-        targets=sample_targets,
+        targets_config=sample_targets.config,
     )
     source_detector = cast(Detector, source_model.detector)
     detector = cast(Detector, api.model.detector)
     classifier_head = cast(ClassifierHead, detector.classifier_head)
 
-    assert api.targets is sample_targets
+    assert api.targets.config == sample_targets.config
     assert detector.num_classes == len(sample_targets.class_names)
     assert (
         classifier_head.classifier.out_channels
@@ -255,6 +258,43 @@ def test_user_can_load_checkpoint_with_new_targets(
         torch.testing.assert_close(target_backbone[key], value)
 
 
+def test_checkpoint_with_same_targets_config_keeps_heads_unchanged(
+    tmp_path: Path,
+) -> None:
+    """User story: same targets config does not rebuild prediction heads."""
+
+    module = build_training_module(model_config=BatDetect2Config().model)
+    trainer = L.Trainer(enable_checkpointing=False, logger=False)
+    checkpoint_path = tmp_path / "same_targets.ckpt"
+    trainer.strategy.connect(module)
+    trainer.save_checkpoint(checkpoint_path)
+
+    source_model, source_model_config = load_model_from_checkpoint(
+        checkpoint_path
+    )
+    source_detector = cast(Detector, source_model.detector)
+
+    api = BatDetect2API.from_checkpoint(
+        checkpoint_path,
+        targets_config=source_model_config.targets,
+    )
+    detector = cast(Detector, api.model.detector)
+
+    for key, value in source_detector.classifier_head.state_dict().items():
+        assert key in detector.classifier_head.state_dict()
+        torch.testing.assert_close(
+            detector.classifier_head.state_dict()[key],
+            value,
+        )
+
+    for key, value in source_detector.bbox_head.state_dict().items():
+        assert key in detector.bbox_head.state_dict()
+        torch.testing.assert_close(
+            detector.bbox_head.state_dict()[key],
+            value,
+        )
+
+
 def test_user_can_finetune_only_heads(
     tmp_path: Path,
     example_annotations,
diff --git a/tests/test_train/test_lightning.py b/tests/test_train/test_lightning.py
index 05f5fea..1ea2e3c 100644
--- a/tests/test_train/test_lightning.py
+++ b/tests/test_train/test_lightning.py
@@ -176,10 +176,10 @@ def test_api_from_checkpoint_reconstructs_model_config(tmp_path: Path):
 
     api = BatDetect2API.from_checkpoint(path)
 
-    assert api.config.model.model_dump(
+    assert api.model_config.model_dump(
         mode="json"
     ) == module.model_config.model_dump(mode="json")
-    assert api.config.audio.samplerate == module.model_config.samplerate
+    assert api.audio_config.samplerate == module.model_config.samplerate
 
 
 def test_train_smoke_produces_loadable_checkpoint(