diff --git a/docs/source/reference/api.md b/docs/source/reference/api.md
index d514bce..916e6df 100644
--- a/docs/source/reference/api.md
+++ b/docs/source/reference/api.md
@@ -2,7 +2,8 @@
 
 `BatDetect2API` is the main entry point for the current Python workflow.
 
-It wraps model loading, inference, evaluation, output formatting, and training-related entry points behind one object.
+It wraps model loading, inference, evaluation, output formatting, and
+training-related entry points behind one object.
 
 Defined in `batdetect2.api_v2`.
 
@@ -10,8 +11,8 @@ Defined in `batdetect2.api_v2`.
 
 - `BatDetect2API.from_checkpoint(path, ...)`
   - load a trained checkpoint and optional config overrides.
-- `BatDetect2API.from_config(config)`
-  - build a full stack from a `BatDetect2Config` object.
+- `BatDetect2API.from_config(model_config=..., targets_config=..., ...)`
+  - build a full stack from separate config objects.
 
 ## Inference methods
 
@@ -46,10 +47,12 @@ Defined in `batdetect2.api_v2`.
 
 ## Output persistence helpers
 
-- `save_predictions(predictions, path, audio_dir=None, format=None, config=None)`
+- `save_predictions(predictions, path, audio_dir=None, format=None,
+  config=None)`
 - `load_predictions(path, format=None, config=None)`
 
-Use these when you want to save programmatic predictions without going through the CLI.
+Use these when you want to save programmatic predictions without going through
+the CLI.
 
 ## Training and evaluation entry points
 
@@ -60,6 +63,9 @@ Use these when you want to save programmatic predictions without going through t
 
 ## Related pages
 
-- Python tutorial: {doc}`../tutorials/integrate-with-a-python-pipeline`
-- Outputs config reference: {doc}`outputs-config`
-- Output formats reference: {doc}`output-formats`
+- Python tutorial:
+  {doc}`../tutorials/integrate-with-a-python-pipeline`
+- Outputs config reference:
+  {doc}`outputs-config`
+- Output formats reference:
+  {doc}`output-formats`
diff --git a/docs/source/reference/app-config.md b/docs/source/reference/app-config.md
deleted file mode 100644
index 1237c0f..0000000
--- a/docs/source/reference/app-config.md
+++ /dev/null
@@ -1,38 +0,0 @@
-# Top-level app config reference
-
-The top-level config object is `BatDetect2Config`.
-
-Defined in `batdetect2.config`.
-
-It combines the main configuration surfaces used across training, inference, evaluation, outputs, and logging.
-
-## Fields
-
-- `config_version`
-- `train`
-  - training-specific config.
-- `evaluation`
-  - evaluation task and plot config.
-- `model`
-  - model architecture, preprocessing, postprocessing, and targets.
-- `audio`
-  - audio loading and resampling config.
-- `inference`
-  - clipping and loader config for prediction-time workflows.
-- `outputs`
-  - output format and output transform config.
-- `logging`
-  - logging backend and formatting config.
-
-## Mental model
-
-Think of `BatDetect2Config` as the complete application wiring for the current stack.
-
-Use it when you want one reproducible config that describes the whole workflow.
-
-## Related pages
-
-- Inference config: {doc}`inference-config`
-- Evaluation config: {doc}`evaluation-config`
-- Outputs config: {doc}`outputs-config`
-- General config reference: {doc}`configs`
diff --git a/docs/source/reference/cli/index.md b/docs/source/reference/cli/index.md
index e52c828..c8a238b 100644
--- a/docs/source/reference/cli/index.md
+++ b/docs/source/reference/cli/index.md
@@ -24,8 +24,8 @@ for full options and argument details.
 - Global CLI options are documented in {doc}`base`.
 - Paths with spaces should be wrapped in quotes.
 - Input audio is expected to be mono.
-- Legacy `detect` uses a required threshold argument, while `predict` uses
-  the optional `--detection-threshold` override.
+- Legacy `detect` uses a required threshold argument, while `predict` uses the
+  optional `--detection-threshold` override.
 
 ```{warning}
 `batdetect2 detect` is a legacy command.
diff --git a/docs/source/reference/configs.rst b/docs/source/reference/configs.rst
index 733159a..90261d1 100644
--- a/docs/source/reference/configs.rst
+++ b/docs/source/reference/configs.rst
@@ -1,5 +1,15 @@
 Config reference
 ================
 
-.. automodule:: batdetect2.config
-   :members:
+BatDetect2 uses separate config objects for different workflow surfaces.
+
+Use the dedicated reference pages for each config family:
+
+- inference config
+- evaluation config
+- outputs config
+- preprocessing config
+- postprocess config
+- targets config workflow
+
+Example config files live under `example_data/configs/`.
diff --git a/docs/source/reference/index.md b/docs/source/reference/index.md
index f0f0beb..cd09bc1 100644
--- a/docs/source/reference/index.md
+++ b/docs/source/reference/index.md
@@ -2,14 +2,14 @@
 
 Reference pages are the detailed lookup pages.
 
-Use this section when you need exact command options, setting names, output details, or Python API entries.
+Use this section when you need exact command options, setting names, output
+details, or Python API entries.
 
 ```{toctree}
 :maxdepth: 1
 
 cli/index
 api
-app-config
 inference-config
 evaluation-config
 outputs-config
diff --git a/example_data/config.yaml b/example_data/config.yaml
deleted file mode 100644
index 0b2ffa3..0000000
--- a/example_data/config.yaml
+++ /dev/null
@@ -1,192 +0,0 @@
-config_version: v1
-
-audio:
-  samplerate: 256000
-  resample:
-    enabled: true
-    method: poly
-
-model:
-  samplerate: 256000
-
-  preprocess:
-    stft:
-      window_duration: 0.002
-      window_overlap: 0.75
-      window_fn: hann
-    frequencies:
-      max_freq: 120000
-      min_freq: 10000
-    size:
-      height: 128
-      resize_factor: 0.5
-    spectrogram_transforms:
-      - name: pcen
-        time_constant: 0.1
-        gain: 0.98
-        bias: 2
-        power: 0.5
-      - name: spectral_mean_subtraction
-
-  architecture:
-    name: UNetBackbone
-    input_height: 128
-    in_channels: 1
-    encoder:
-      layers:
-        - name: FreqCoordConvDown
-          out_channels: 32
-        - name: FreqCoordConvDown
-          out_channels: 64
-        - name: LayerGroup
-          layers:
-            - name: FreqCoordConvDown
-              out_channels: 128
-            - name: ConvBlock
-              out_channels: 256
-    bottleneck:
-      channels: 256
-      layers:
-        - name: SelfAttention
-          attention_channels: 256
-    decoder:
-      layers:
-        - name: FreqCoordConvUp
-          out_channels: 64
-        - name: FreqCoordConvUp
-          out_channels: 32
-        - name: LayerGroup
-          layers:
-            - name: FreqCoordConvUp
-              out_channels: 32
-            - name: ConvBlock
-              out_channels: 32
-
-  postprocess:
-    nms_kernel_size: 9
-    detection_threshold: 0.01
-    top_k_per_sec: 200
-
-train:
-  optimizer:
-    name: adam
-    learning_rate: 0.001
-
-  scheduler:
-    name: cosine_annealing
-    t_max: 100
-
-  labels:
-    sigma: 3
-
-  trainer:
-    max_epochs: 10
-    check_val_every_n_epoch: 5
-
-  train_loader:
-    batch_size: 8
-    shuffle: true
-
-    clipping_strategy:
-      name: random_subclip
-      duration: 0.256
-
-    augmentations:
-      enabled: true
-      audio:
-        - name: mix_audio
-          probability: 0.2
-          min_weight: 0.3
-          max_weight: 0.7
-        - name: add_echo
-          probability: 0.2
-          max_delay: 0.005
-          min_weight: 0.0
-          max_weight: 1.0
-      spectrogram:
-        - name: scale_volume
-          probability: 0.2
-          min_scaling: 0.0
-          max_scaling: 2.0
-        - name: warp
-          probability: 0.2
-          delta: 0.04
-        - name: mask_time
-          probability: 0.2
-          max_perc: 0.05
-          max_masks: 3
-        - name: mask_freq
-          probability: 0.2
-          max_perc: 0.10
-          max_masks: 3
-
-  val_loader:
-    clipping_strategy:
-      name: whole_audio_padded
-      chunk_size: 0.256
-
-  loss:
-    detection:
-      weight: 1.0
-      focal:
-        beta: 4
-        alpha: 2
-    classification:
-      weight: 2.0
-      focal:
-        beta: 4
-        alpha: 2
-    size:
-      weight: 0.1
-
-  validation:
-    tasks:
-      - name: sound_event_detection
-        metrics:
-          - name: average_precision
-      - name: sound_event_classification
-        metrics:
-          - name: average_precision
-
-logging:
-  train:
-    name: csv
-
-evaluation:
-  tasks:
-    - name: sound_event_detection
-      metrics:
-        - name: average_precision
-        - name: roc_auc
-      plots:
-        - name: pr_curve
-        - name: score_distribution
-        - name: example_detection
-    - name: sound_event_classification
-      metrics:
-        - name: average_precision
-        - name: roc_auc
-      plots:
-        - name: pr_curve
-    - name: top_class_detection
-      metrics:
-        - name: average_precision
-      plots:
-        - name: pr_curve
-        - name: confusion_matrix
-        - name: example_classification
-    - name: clip_detection
-      metrics:
-        - name: average_precision
-        - name: roc_auc
-      plots:
-        - name: pr_curve
-        - name: roc_curve
-        - name: score_distribution
-    - name: clip_classification
-      metrics:
-        - name: average_precision
-        - name: roc_auc
-      plots:
-        - name: pr_curve
-        - name: roc_curve
diff --git a/example_data/configs/audio.yaml b/example_data/configs/audio.yaml
new file mode 100644
index 0000000..0100572
--- /dev/null
+++ b/example_data/configs/audio.yaml
@@ -0,0 +1,4 @@
+samplerate: 256000
+resample:
+  enabled: true
+  method: poly
diff --git a/example_data/configs/evaluation.yaml b/example_data/configs/evaluation.yaml
new file mode 100644
index 0000000..f2577ae
--- /dev/null
+++ b/example_data/configs/evaluation.yaml
@@ -0,0 +1,37 @@
+tasks:
+  - name: sound_event_detection
+    metrics:
+      - name: average_precision
+      - name: roc_auc
+    plots:
+      - name: pr_curve
+      - name: score_distribution
+      - name: example_detection
+  - name: sound_event_classification
+    metrics:
+      - name: average_precision
+      - name: roc_auc
+    plots:
+      - name: pr_curve
+  - name: top_class_detection
+    metrics:
+      - name: average_precision
+    plots:
+      - name: pr_curve
+      - name: confusion_matrix
+      - name: example_classification
+  - name: clip_detection
+    metrics:
+      - name: average_precision
+      - name: roc_auc
+    plots:
+      - name: pr_curve
+      - name: roc_curve
+      - name: score_distribution
+  - name: clip_classification
+    metrics:
+      - name: average_precision
+      - name: roc_auc
+    plots:
+      - name: pr_curve
+      - name: roc_curve
diff --git a/example_data/configs/inference.yaml b/example_data/configs/inference.yaml
new file mode 100644
index 0000000..f9a3078
--- /dev/null
+++ b/example_data/configs/inference.yaml
@@ -0,0 +1,9 @@
+loader:
+  batch_size: 8
+
+clipping:
+  enabled: true
+  duration: 0.5
+  overlap: 0.0
+  max_empty: 0.0
+  discard_empty: true
diff --git a/example_data/configs/logging.yaml b/example_data/configs/logging.yaml
new file mode 100644
index 0000000..bb5f366
--- /dev/null
+++ b/example_data/configs/logging.yaml
@@ -0,0 +1,2 @@
+train:
+  name: csv
diff --git a/example_data/configs/model.yaml b/example_data/configs/model.yaml
new file mode 100644
index 0000000..b03a525
--- /dev/null
+++ b/example_data/configs/model.yaml
@@ -0,0 +1,59 @@
+samplerate: 256000
+
+preprocess:
+  stft:
+    window_duration: 0.002
+    window_overlap: 0.75
+    window_fn: hann
+  frequencies:
+    max_freq: 120000
+    min_freq: 10000
+  size:
+    height: 128
+    resize_factor: 0.5
+  spectrogram_transforms:
+    - name: pcen
+      time_constant: 0.1
+      gain: 0.98
+      bias: 2
+      power: 0.5
+    - name: spectral_mean_subtraction
+
+architecture:
+  name: UNetBackbone
+  input_height: 128
+  in_channels: 1
+  encoder:
+    layers:
+      - name: FreqCoordConvDown
+        out_channels: 32
+      - name: FreqCoordConvDown
+        out_channels: 64
+      - name: LayerGroup
+        layers:
+          - name: FreqCoordConvDown
+            out_channels: 128
+          - name: ConvBlock
+            out_channels: 256
+  bottleneck:
+    channels: 256
+    layers:
+      - name: SelfAttention
+        attention_channels: 256
+  decoder:
+    layers:
+      - name: FreqCoordConvUp
+        out_channels: 64
+      - name: FreqCoordConvUp
+        out_channels: 32
+      - name: LayerGroup
+        layers:
+          - name: FreqCoordConvUp
+            out_channels: 32
+          - name: ConvBlock
+            out_channels: 32
+
+postprocess:
+  nms_kernel_size: 9
+  detection_threshold: 0.01
+  top_k_per_sec: 200
diff --git a/example_data/configs/outputs.yaml b/example_data/configs/outputs.yaml
new file mode 100644
index 0000000..458093a
--- /dev/null
+++ b/example_data/configs/outputs.yaml
@@ -0,0 +1,9 @@
+format:
+  name: raw
+  include_class_scores: true
+  include_features: true
+  include_geometry: true
+
+transform:
+  detection_transforms: []
+  clip_transforms: []
diff --git a/example_data/configs/training.yaml b/example_data/configs/training.yaml
new file mode 100644
index 0000000..b99899e
--- /dev/null
+++ b/example_data/configs/training.yaml
@@ -0,0 +1,79 @@
+optimizer:
+  name: adam
+  learning_rate: 0.001
+
+scheduler:
+  name: cosine_annealing
+  t_max: 100
+
+labels:
+  sigma: 3
+
+trainer:
+  max_epochs: 10
+  check_val_every_n_epoch: 5
+
+train_loader:
+  batch_size: 8
+  shuffle: true
+
+  clipping_strategy:
+    name: random_subclip
+    duration: 0.256
+
+  augmentations:
+    enabled: true
+    audio:
+      - name: mix_audio
+        probability: 0.2
+        min_weight: 0.3
+        max_weight: 0.7
+      - name: add_echo
+        probability: 0.2
+        max_delay: 0.005
+        min_weight: 0.0
+        max_weight: 1.0
+    spectrogram:
+      - name: scale_volume
+        probability: 0.2
+        min_scaling: 0.0
+        max_scaling: 2.0
+      - name: warp
+        probability: 0.2
+        delta: 0.04
+      - name: mask_time
+        probability: 0.2
+        max_perc: 0.05
+        max_masks: 3
+      - name: mask_freq
+        probability: 0.2
+        max_perc: 0.10
+        max_masks: 3
+
+val_loader:
+  clipping_strategy:
+    name: whole_audio_padded
+    chunk_size: 0.256
+
+loss:
+  detection:
+    weight: 1.0
+    focal:
+      beta: 4
+      alpha: 2
+  classification:
+    weight: 2.0
+    focal:
+      beta: 4
+      alpha: 2
+  size:
+    weight: 0.1
+
+validation:
+  tasks:
+    - name: sound_event_detection
+      metrics:
+        - name: average_precision
+    - name: sound_event_classification
+      metrics:
+        - name: average_precision
diff --git a/justfile b/justfile
index f8d298a..0e1b870 100644
--- a/justfile
+++ b/justfile
@@ -112,6 +112,14 @@ clean: clean-build clean-pyc clean-test clean-docs
 example-train OPTIONS="":
     uv run batdetect2 train \
         --val-dataset example_data/dataset.yaml \
-        --config example_data/config.yaml \
+        --base-dir . \
+        --targets example_data/targets.yaml \
+        --model-config example_data/configs/model.yaml \
+        --training-config example_data/configs/training.yaml \
+        --audio-config example_data/configs/audio.yaml \
+        --evaluation-config example_data/configs/evaluation.yaml \
+        --inference-config example_data/configs/inference.yaml \
+        --outputs-config example_data/configs/outputs.yaml \
+        --logging-config example_data/configs/logging.yaml \
         {{OPTIONS}} \
         example_data/dataset.yaml
diff --git a/src/batdetect2/config.py b/src/batdetect2/config.py
deleted file mode 100644
index 88b23ee..0000000
--- a/src/batdetect2/config.py
+++ /dev/null
@@ -1,33 +0,0 @@
-from typing import Literal
-
-from pydantic import Field
-
-from batdetect2.audio import AudioConfig
-from batdetect2.core.configs import BaseConfig
-from batdetect2.evaluate.config import (
-    EvaluationConfig,
-    get_default_eval_config,
-)
-from batdetect2.inference.config import InferenceConfig
-from batdetect2.logging import AppLoggingConfig
-from batdetect2.models import ModelConfig
-from batdetect2.outputs import OutputsConfig
-from batdetect2.targets import TargetConfig
-from batdetect2.train.config import TrainingConfig
-
-__all__ = ["BatDetect2Config"]
-
-
-class BatDetect2Config(BaseConfig):
-    config_version: Literal["v1"] = "v1"
-
-    train: TrainingConfig = Field(default_factory=TrainingConfig)
-    evaluation: EvaluationConfig = Field(
-        default_factory=get_default_eval_config
-    )
-    model: ModelConfig = Field(default_factory=ModelConfig)
-    targets: TargetConfig = Field(default_factory=TargetConfig)
-    audio: AudioConfig = Field(default_factory=AudioConfig)
-    inference: InferenceConfig = Field(default_factory=InferenceConfig)
-    outputs: OutputsConfig = Field(default_factory=OutputsConfig)
-    logging: AppLoggingConfig = Field(default_factory=AppLoggingConfig)
diff --git a/tests/test_models/test_backbones.py b/tests/test_models/test_backbones.py
index 6f26dad..9f121f9 100644
--- a/tests/test_models/test_backbones.py
+++ b/tests/test_models/test_backbones.py
@@ -203,8 +203,8 @@ in_channels: 1
 def test_load_backbone_config_from_example_data(example_data_dir: Path):
     """load_backbone_config loads the real example config correctly."""
     config = load_backbone_config(
-        example_data_dir / "config.yaml",
-        field="model.architecture",
+        example_data_dir / "configs" / "model.yaml",
+        field="architecture",
     )
 
     assert isinstance(config, UNetBackboneConfig)
diff --git a/tests/test_train/test_checkpoints.py b/tests/test_train/test_checkpoints.py
index b228378..3603cac 100644
--- a/tests/test_train/test_checkpoints.py
+++ b/tests/test_train/test_checkpoints.py
@@ -3,20 +3,19 @@ from pathlib import Path
 import pytest
 from soundevent import data
 
-from batdetect2.config import BatDetect2Config
-from batdetect2.train import run_train
+from batdetect2.train import TrainingConfig, run_train
 
 pytestmark = pytest.mark.slow
 
 
-def _build_fast_train_config() -> BatDetect2Config:
-    config = BatDetect2Config()
-    config.train.trainer.limit_train_batches = 1
-    config.train.trainer.limit_val_batches = 1
-    config.train.trainer.log_every_n_steps = 1
-    config.train.trainer.check_val_every_n_epoch = 1
-    config.train.train_loader.batch_size = 1
-    config.train.train_loader.augmentations.enabled = False
+def _build_fast_train_config() -> TrainingConfig:
+    config = TrainingConfig()
+    config.trainer.limit_train_batches = 1
+    config.trainer.limit_val_batches = 1
+    config.trainer.log_every_n_steps = 1
+    config.trainer.check_val_every_n_epoch = 1
+    config.train_loader.batch_size = 1
+    config.train_loader.augmentations.enabled = False
     return config
 
 
@@ -29,9 +28,7 @@ def test_train_saves_checkpoint_in_requested_experiment_run_dir(
     run_train(
         train_annotations=example_annotations[:1],
         val_annotations=example_annotations[:1],
-        train_config=config.train,
-        model_config=config.model,
-        audio_config=config.audio,
+        train_config=config,
         num_epochs=1,
         train_workers=0,
         val_workers=0,
@@ -50,14 +47,12 @@ def test_train_without_validation_can_still_save_last_checkpoint(
     example_annotations: list[data.ClipAnnotation],
 ) -> None:
     config = _build_fast_train_config()
-    config.train.checkpoints.save_last = True
+    config.checkpoints.save_last = True
 
     run_train(
         train_annotations=example_annotations[:1],
         val_annotations=None,
-        train_config=config.train,
-        model_config=config.model,
-        audio_config=config.audio,
+        train_config=config,
         num_epochs=1,
         train_workers=0,
         val_workers=0,
@@ -73,16 +68,14 @@ def test_train_controls_which_checkpoints_are_kept(
     example_annotations: list[data.ClipAnnotation],
 ) -> None:
     config = _build_fast_train_config()
-    config.train.checkpoints.save_top_k = 1
-    config.train.checkpoints.save_last = True
-    config.train.checkpoints.filename = "epoch{epoch}"
+    config.checkpoints.save_top_k = 1
+    config.checkpoints.save_last = True
+    config.checkpoints.filename = "epoch{epoch}"
 
     run_train(
         train_annotations=example_annotations[:1],
         val_annotations=example_annotations[:1],
-        train_config=config.train,
-        model_config=config.model,
-        audio_config=config.audio,
+        train_config=config,
         num_epochs=3,
         train_workers=0,
         val_workers=0,
diff --git a/tests/test_train/test_config.py b/tests/test_train/test_config.py
index 1384887..547e64f 100644
--- a/tests/test_train/test_config.py
+++ b/tests/test_train/test_config.py
@@ -1,12 +1,43 @@
-from batdetect2.config import BatDetect2Config
-from batdetect2.core import load_config
+from batdetect2.audio import AudioConfig
+from batdetect2.evaluate import EvaluationConfig
+from batdetect2.inference import InferenceConfig
+from batdetect2.logging import AppLoggingConfig
+from batdetect2.models import ModelConfig
+from batdetect2.outputs import OutputsConfig
+from batdetect2.targets import TargetConfig
+from batdetect2.train import TrainingConfig
 
 
-def test_example_config_is_valid(example_data_dir):
-    conf = load_config(
-        example_data_dir / "config.yaml",
-        schema=BatDetect2Config,
-        extra="forbid",
-        strict=True,
+def test_example_split_configs_are_valid(example_data_dir):
+    configs_dir = example_data_dir / "configs"
+
+    assert isinstance(
+        AudioConfig.load(configs_dir / "audio.yaml"), AudioConfig
+    )
+    assert isinstance(
+        ModelConfig.load(configs_dir / "model.yaml"), ModelConfig
+    )
+    assert isinstance(
+        TargetConfig.load(example_data_dir / "targets.yaml"),
+        TargetConfig,
+    )
+    assert isinstance(
+        TrainingConfig.load(configs_dir / "training.yaml"),
+        TrainingConfig,
+    )
+    assert isinstance(
+        EvaluationConfig.load(configs_dir / "evaluation.yaml"),
+        EvaluationConfig,
+    )
+    assert isinstance(
+        InferenceConfig.load(configs_dir / "inference.yaml"),
+        InferenceConfig,
+    )
+    assert isinstance(
+        OutputsConfig.load(configs_dir / "outputs.yaml"),
+        OutputsConfig,
+    )
+    assert isinstance(
+        AppLoggingConfig.load(configs_dir / "logging.yaml"),
+        AppLoggingConfig,
     )
-    assert isinstance(conf, BatDetect2Config)