diff --git a/README.md b/README.md
index 32ad0a8..1f37550 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,6 @@ runs:
 
 baselines:
   - baseline:
-      baseline_id: COSMO-E
       label: COSMO-E
       root: /store_new/mch/msopr/ml/COSMO-E
       steps: 0/120/6
diff --git a/config/forecasters-co1e.yaml b/config/forecasters-co1e.yaml
index 83846ec..3997ffe 100644
--- a/config/forecasters-co1e.yaml
+++ b/config/forecasters-co1e.yaml
@@ -20,9 +20,7 @@ runs:
       extra_requirements:
         - git+https://github.com/ecmwf/anemoi-inference.git@0.6.3
 
-baselines:
   - baseline:
-      baseline_id: COSMO-1E
       label: COSMO-1E
       root: /store_new/mch/msopr/ml/COSMO-1E
       steps: 0/33/6
diff --git a/config/forecasters-co2-disentangled.yaml b/config/forecasters-co2-disentangled.yaml
index c9a75f2..63178ae 100644
--- a/config/forecasters-co2-disentangled.yaml
+++ b/config/forecasters-co2-disentangled.yaml
@@ -41,9 +41,7 @@ runs:
         - earthkit-data<0.19.0
         - git+https://github.com/MeteoSwiss/anemoi-core.git@2a90165e3f25defc55fbeb77f7b4ebfef685820d#subdirectory=models
 
-baselines:
   - baseline:
-      baseline_id: COSMO-E
       label: COSMO-E
       root: /store_new/mch/msopr/ml/COSMO-E
       steps: 0/120/6
diff --git a/config/forecasters-co2.yaml b/config/forecasters-co2.yaml
index 059ab97..e9aeb8d 100644
--- a/config/forecasters-co2.yaml
+++ b/config/forecasters-co2.yaml
@@ -16,9 +16,7 @@ runs:
       extra_requirements:
         - git+https://github.com/ecmwf/anemoi-inference.git@0.8.3
 
-baselines:
   - baseline:
-      baseline_id: COSMO-E
       label: COSMO-E
       root: /store_new/mch/msopr/ml/COSMO-E
       steps: 0/120/6
diff --git a/config/forecasters-ich1-oper-fixed.yaml b/config/forecasters-ich1-oper-fixed.yaml
index 7eb5709..bd4a6f5 100644
--- a/config/forecasters-ich1-oper-fixed.yaml
+++ b/config/forecasters-ich1-oper-fixed.yaml
@@ -33,7 +33,6 @@ runs:
 
 baselines:
   - baseline:
-      baseline_id: ICON-CH1-EPS
       label: ICON-CH1-EPS
       root: /store_new/mch/msopr/ml/ICON-CH1-EPS
       steps: 0/33/6
diff --git a/config/forecasters-ich1-oper.yaml b/config/forecasters-ich1-oper.yaml
index 6e5b011..b8db4cc 100644
--- a/config/forecasters-ich1-oper.yaml
+++ b/config/forecasters-ich1-oper.yaml
@@ -22,14 +22,12 @@ runs:
         - earthkit-data<0.19.0
         - git+https://github.com/ecmwf/anemoi-inference.git@main
 
-baselines:
   - baseline:
-      baseline_id: ICON-CH1-EPS
       label: ICON-CH1-ctrl
       root: /scratch/mch/cmerker/ICON-CH1-EPS
       steps: 0/33/6
+
   - baseline:
-      baseline_id: ICON-CH2-EPS
       label: ICON-CH2-ctrl
       root: /scratch/mch/cmerker/ICON-CH2-EPS
       steps: 0/120/6
diff --git a/config/forecasters-ich1.yaml b/config/forecasters-ich1.yaml
index a5de9b5..3e8a965 100644
--- a/config/forecasters-ich1.yaml
+++ b/config/forecasters-ich1.yaml
@@ -35,13 +35,11 @@ runs:
   #     config: resources/inference/configs/sgm-forecaster-global-ich1.yaml
   #     disable_local_eccodes_definitions: true
   #     extra_requirements:
-        # - earthkit-utils<0.2.0
-        # - earthkit-data<0.19.0
-        # - git+https://github.com/ecmwf/anemoi-inference.git@main
+  #       - earthkit-utils<0.2.0
+  #       - earthkit-data<0.19.0
+  #       - git+https://github.com/ecmwf/anemoi-inference.git@main
 
-baselines:
   - baseline:
-      baseline_id: ICON-CH2-EPS
       label: ICON-CH2-EPS
       root: /scratch/mch/cmerker/ICON-CH2-EPS
       steps: 0/120/6
diff --git a/config/interpolators-co2.yaml b/config/interpolators-co2.yaml
index 115dd6b..cbece18 100644
--- a/config/interpolators-co2.yaml
+++ b/config/interpolators-co2.yaml
@@ -47,9 +47,7 @@ runs:
       extra_requirements:
         - git+https://github.com/ecmwf/anemoi-inference.git@0.8.3
 
-baselines:
   - baseline:
-      baseline_id: COSMO-E-1h
       label: COSMO-E
       root: /store_new/mch/msopr/ml/COSMO-E_hourly
       steps: 0/120/1
diff --git a/src/evalml/config.py b/src/evalml/config.py
index 802afab..b1b7eab 100644
--- a/src/evalml/config.py
+++ b/src/evalml/config.py
@@ -151,10 +151,10 @@ class InterpolatorConfig(RunConfig):
 class BaselineConfig(BaseModel):
     """Configuration for a single baseline to include in the verification."""
 
-    baseline_id: str = Field(
-        ...,
+    baseline_id: str | None = Field(
+        None,
         min_length=1,
-        description="Identifier for the baseline, e.g. 'COSMO-E'.",
+        description="Deprecated compatibility field. Workflow baseline IDs are derived from the stem of `root`.",
     )
     label: str = Field(
         ...,
@@ -164,7 +164,7 @@ class BaselineConfig(BaseModel):
     root: str = Field(
         ...,
         min_length=1,
-        description="Root directory where the baseline data is stored.",
+        description="Root directory where the baseline data is stored. The workflow derives the baseline ID from the stem of this path.",
     )
     steps: str = Field(
         ...,
@@ -298,13 +298,13 @@ class ConfigModel(BaseModel):
         description="Optional label for the experiment that will be used in the experiment directory name. Defaults to the config file name if not provided.",
     )
     dates: Dates | ExplicitDates
-    runs: List[ForecasterItem | InterpolatorItem] = Field(
+    runs: List[ForecasterItem | InterpolatorItem | BaselineItem] = Field(
         ...,
-        description="Dictionary of runs to execute, with run IDs as keys and configurations as values.",
+        description="List of experiment participants, including forecaster/interpolator ML runs and baselines.",
     )
     baselines: List[BaselineItem] = Field(
-        ...,
-        description="Dictionary of baselines to include in the verification.",
+        default_factory=list,
+        description="Deprecated top-level baselines list. Prefer defining baseline entries directly in `runs`.",
     )
     truth: TruthConfig | None
     stratification: Stratification
diff --git a/tests/unit/test_config.py b/tests/unit/test_config.py
index 6b452b0..40281a6 100644
--- a/tests/unit/test_config.py
+++ b/tests/unit/test_config.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import pytest
 
 from evalml.config import ConfigModel
@@ -25,3 +27,67 @@ def test_example_interpolators_config(example_interpolators_config):
     del example_interpolators_config["runs"]
     with pytest.raises(ValueError, match="Field required"):
         _ = ConfigModel.model_validate(example_interpolators_config)
+
+
+def test_legacy_top_level_baselines_still_supported(example_forecasters_config):
+    """Top-level `baselines` remains accepted for backward compatibility."""
+
+    cfg = {k: v for k, v in example_forecasters_config.items() if k != "runs"}
+    cfg["runs"] = [
+        run for run in example_forecasters_config["runs"] if "forecaster" in run
+    ]
+    cfg["baselines"] = [
+        run for run in example_forecasters_config["runs"] if "baseline" in run
+    ]
+
+    _ = ConfigModel.model_validate(cfg)
+
+
+def test_workflow_parsing_excludes_baselines_from_run_configs(
+    example_forecasters_config,
+):
+    """Baseline entries in `runs` should not be treated as ML run configs."""
+
+    namespace = {
+        "Path": Path,
+        "config": example_forecasters_config,
+    }
+    common_rules = Path("workflow/rules/common.smk").read_text()
+
+    exec(common_rules, namespace)
+
+    run_configs = namespace["RUN_CONFIGS"]
+    baseline_configs = namespace["BASELINE_CONFIGS"]
+
+    assert all(
+        run_config["model_type"] != "baseline" for run_config in run_configs.values()
+    )
+    assert baseline_configs == {
+        "COSMO-E": {
+            "label": "COSMO-E",
+            "root": "/store_new/mch/msopr/ml/COSMO-E",
+            "steps": "0/120/6",
+        }
+    }
+
+
+def test_workflow_derives_baseline_id_from_root_stem(example_interpolators_config):
+    """Workflow baseline IDs should come from the baseline root path stem."""
+
+    namespace = {
+        "Path": Path,
+        "config": example_interpolators_config,
+    }
+    common_rules = Path("workflow/rules/common.smk").read_text()
+
+    exec(common_rules, namespace)
+
+    baseline_configs = namespace["BASELINE_CONFIGS"]
+
+    assert "COSMO-E_hourly" in baseline_configs
+    assert "COSMO-E-1h" not in baseline_configs
+    assert baseline_configs["COSMO-E_hourly"] == {
+        "label": "COSMO-E",
+        "root": "/store_new/mch/msopr/ml/COSMO-E_hourly",
+        "steps": "0/120/1",
+    }
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 9fe6ff0..3b5062e 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -141,6 +141,8 @@ def collect_all_runs() -> dict:
     runs: dict[str, dict] = {}
     for run_entry in config["runs"]:
         model_type = next(iter(run_entry))
+        if model_type == "baseline":
+            continue
         run_config = run_entry[model_type]
         runs |= register_run(model_type, run_config)
     return runs
@@ -159,11 +161,22 @@ def collect_all_candidates():
 def collect_all_baselines():
     """Collect all baselines defined in the configuration."""
     baselines = {}
-    for baseline_entry in copy.deepcopy(config["baselines"]):
+
+    for run_entry in copy.deepcopy(config["runs"]):
+        if "baseline" not in run_entry:
+            continue
+        baseline_config = run_entry["baseline"]
+        baseline_id = Path(baseline_config["root"]).stem
+        baselines[baseline_id] = baseline_config
+
+    # Backward compatibility with legacy top-level `baselines` block.
+    for baseline_entry in copy.deepcopy(config.get("baselines", [])):
         baseline_type = next(iter(baseline_entry))
         baseline_config = baseline_entry[baseline_type]
-        baseline_id = baseline_config.pop("baseline_id")
+        baseline_id = Path(baseline_config["root"]).stem
+        baseline_config.pop("baseline_id", None)
         baselines[baseline_id] = baseline_config
+
     return baselines
 
 
diff --git a/workflow/tools/config.schema.json b/workflow/tools/config.schema.json
index cc66d7f..20f6512 100644
--- a/workflow/tools/config.schema.json
+++ b/workflow/tools/config.schema.json
@@ -4,10 +4,18 @@
       "description": "Configuration for a single baseline to include in the verification.",
       "properties": {
         "baseline_id": {
-          "description": "Identifier for the baseline, e.g. 'COSMO-E'.",
-          "minLength": 1,
-          "title": "Baseline Id",
-          "type": "string"
+          "anyOf": [
+            {
+              "minLength": 1,
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "Deprecated compatibility field. Workflow baseline IDs are derived from the stem of `root`.",
+          "title": "Baseline Id"
         },
         "label": {
           "description": "Label for the baseline that will be used in experiment results such as reports and figures.",
@@ -16,7 +24,7 @@
           "type": "string"
         },
         "root": {
-          "description": "Root directory where the baseline data is stored.",
+          "description": "Root directory where the baseline data is stored. The workflow derives the baseline ID from the stem of this path.",
           "minLength": 1,
           "title": "Root",
           "type": "string"
@@ -29,7 +37,6 @@
         }
       },
       "required": [
-        "baseline_id",
         "label",
         "root",
         "steps"
@@ -539,7 +546,7 @@
       "title": "Dates"
     },
     "runs": {
-      "description": "Dictionary of runs to execute, with run IDs as keys and configurations as values.",
+      "description": "List of experiment participants, including forecaster/interpolator ML runs and baselines.",
       "items": {
         "anyOf": [
           {
@@ -547,6 +554,9 @@
           },
           {
             "$ref": "#/$defs/InterpolatorItem"
+          },
+          {
+            "$ref": "#/$defs/BaselineItem"
           }
         ]
       },
@@ -554,7 +564,7 @@
       "type": "array"
     },
     "baselines": {
-      "description": "Dictionary of baselines to include in the verification.",
+      "description": "Deprecated top-level baselines list. Prefer defining baseline entries directly in `runs`.",
       "items": {
         "$ref": "#/$defs/BaselineItem"
       },
@@ -585,7 +595,6 @@
     "description",
     "dates",
     "runs",
-    "baselines",
     "truth",
     "stratification",
     "locations",