diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2ab21e96..371f0e3c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -34,10 +34,16 @@
   `pi`/`e`, and prints floats without loss of precision. PEtab v2 condition
   and measurement tables now write expressions in PEtab syntax
   (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/545)
+* `petab.v2.ProblemConfig.to_yaml` no longer writes empty optional entries
+  (`condition_files`, `experiment_files`, `mapping_files`, `extensions`)
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/547)
 
 **Features**
 * `petab1to2` and `petab_files_1to2` can skip validation via `validate=False`
   (by @FFroehlich in https://github.com/PEtab-dev/libpetab-python/pull/534)
+* Added `petab.v2.C.PROBLEM_CONFIG_REQUIRED_KEYS` and
+  `petab.v2.C.PROBLEM_CONFIG_OPTIONAL_KEYS`
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/547)
 
 ## 0.9 series
 
diff --git a/petab/v2/C.py b/petab/v2/C.py
index d738804f..625f128d 100644
--- a/petab/v2/C.py
+++ b/petab/v2/C.py
@@ -234,6 +234,8 @@
 # YAML
 #: PEtab version key in the YAML file
 FORMAT_VERSION = "format_version"
+#: Problem ID key in the YAML file
+PROBLEM_ID = "id"
 #: Parameter files key in the YAML file
 PARAMETER_FILES = "parameter_files"
 #: Problems key in the YAML file
@@ -261,6 +263,23 @@
 #: PEtab SciML extension
 EXT_ID_SCIML = "sciml"
 
+#: Required top-level keys in the problem YAML file
+PROBLEM_CONFIG_REQUIRED_KEYS = [
+    FORMAT_VERSION,
+    PARAMETER_FILES,
+    MODEL_FILES,
+    OBSERVABLE_FILES,
+    MEASUREMENT_FILES,
+]
+#: Optional top-level keys in the problem YAML file
+PROBLEM_CONFIG_OPTIONAL_KEYS = [
+    PROBLEM_ID,
+    CONDITION_FILES,
+    EXPERIMENT_FILES,
+    MAPPING_FILES,
+    EXTENSIONS,
+]
+
 
 # MAPPING
 
diff --git a/petab/v2/core.py b/petab/v2/core.py
index c36076ab..d7a36a3d 100644
--- a/petab/v2/core.py
+++ b/petab/v2/core.py
@@ -2812,14 +2812,20 @@ def to_yaml(self, filename: str | Path):
             data["model_files"][model_id][C.MODEL_LOCATION] = str(
                 data["model_files"][model_id][C.MODEL_LOCATION]
             )
-        if data["id"] is None:
+        if data[C.PROBLEM_ID] is None:
             # The schema requires a valid id or no id field at all.
-            del data["id"]
+            del data[C.PROBLEM_ID]
 
         for ext_id in list(data[C.EXTENSIONS]):
             if ext_id == C.EXT_ID_SCIML:
                 data[C.EXTENSIONS][ext_id] = self.extensions[ext_id].to_yaml()
 
+        # Omit empty optional entries. Required ones are kept even if empty.
+        for key in C.PROBLEM_CONFIG_OPTIONAL_KEYS:
+            # an empty `id` is invalid and must not be dropped silently
+            if key != C.PROBLEM_ID and not data[key]:
+                del data[key]
+
         write_yaml(data, filename)
 
     @property
diff --git a/tests/v2/test_core.py b/tests/v2/test_core.py
index 4dee46fa..1f13e411 100644
--- a/tests/v2/test_core.py
+++ b/tests/v2/test_core.py
@@ -29,7 +29,7 @@
     UPPER_BOUND,
 )
 from petab.v2.core import *
-from petab.v2.core import ExtensionConfig
+from petab.v2.core import ExtensionConfig, ModelFile
 from petab.v2.lint import CheckUnusedConditions, ValidationIssueSeverity
 from petab.v2.models.sbml_model import SbmlModel
 from petab.v2.petab1to2 import petab1to2
@@ -780,6 +780,62 @@ def test_problem_config_extensions_rejects_non_dict():
         )
 
 
+def test_problem_config_keys_match_schema():
+    """The required/optional YAML keys in `C` match the PEtab v2 schema."""
+    from petab.v1.yaml import SCHEMAS, load_yaml
+
+    schema = load_yaml(SCHEMAS[(2, 0)])
+    assert set(C.PROBLEM_CONFIG_REQUIRED_KEYS) == set(schema["required"])
+    assert set(C.PROBLEM_CONFIG_OPTIONAL_KEYS) == set(
+        schema["properties"]
+    ) - set(schema["required"])
+
+
+def test_problem_config_to_yaml_omits_empty_optional(tmp_path):
+    """Empty optional entries are not written; empty required ones are."""
+    from petab.v1.yaml import load_yaml, validate_yaml_syntax
+
+    pc = ProblemConfig(
+        parameter_files=["parameters.tsv"],
+        model_files={
+            "model": ModelFile(location="model.xml", language="sbml")
+        },
+        measurement_files=["measurements.tsv"],
+    )
+    yaml_path = tmp_path / "problem.yaml"
+    pc.to_yaml(yaml_path)
+
+    yaml_config = load_yaml(yaml_path)
+    assert set(yaml_config) == {
+        C.FORMAT_VERSION,
+        C.PARAMETER_FILES,
+        C.MODEL_FILES,
+        C.MEASUREMENT_FILES,
+        C.OBSERVABLE_FILES,
+    }
+    assert yaml_config[C.OBSERVABLE_FILES] == []
+    validate_yaml_syntax(yaml_config)
+    reloaded = ProblemConfig(**yaml_config, base_path=tmp_path)
+    assert reloaded.model_dump() == pc.model_dump()
+
+    # non-empty optional entries are kept
+    pc.condition_files = ["conditions.tsv"]
+    pc.experiment_files = ["experiments.tsv"]
+    pc.mapping_files = ["mapping.tsv"]
+    pc.extensions = {"my_ext": {"version": "1.0.0", "required": False}}
+    pc.to_yaml(yaml_path)
+
+    yaml_config = load_yaml(yaml_path)
+    assert yaml_config[C.CONDITION_FILES] == ["conditions.tsv"]
+    assert yaml_config[C.EXPERIMENT_FILES] == ["experiments.tsv"]
+    assert yaml_config[C.MAPPING_FILES] == ["mapping.tsv"]
+    assert yaml_config[C.EXTENSIONS] == {
+        "my_ext": {"version": "1.0.0", "required": False}
+    }
+    reloaded = ProblemConfig(**yaml_config, base_path=tmp_path)
+    assert reloaded.model_dump() == pc.model_dump()
+
+
 def test_validate_unsupported_extension_severity():
     """libpetab-python doesn't mathematically interpret extensions, so an
     unsupported extension only ever produces a WARNING (that the problem