diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
index fe61374..6aae64f 100644
--- a/.github/workflows/cd.yml
+++ b/.github/workflows/cd.yml
@@ -21,10 +21,10 @@ jobs:
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Build and push
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: ./Dockerfile
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 00f9460..17bf55d 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -35,6 +35,6 @@ jobs:
         coverage run -m pytest
         coverage lcov -o ./coverage/lcov.info
     - name: Coveralls GitHub Action
-      uses: coverallsapp/github-action@v2.2.1
+      uses: coverallsapp/github-action@v2.2.3
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file
diff --git a/bagel/cli.py b/bagel/cli.py
index d0e548e..47288be 100644
--- a/bagel/cli.py
+++ b/bagel/cli.py
@@ -9,7 +9,7 @@
 import bagel.bids_utils as butil
 import bagel.pheno_utils as putil
 from bagel import mappings, models
-from bagel.utility import load_json
+from bagel.utility import check_overwrite, load_json
 
 bagel = typer.Typer()
 
@@ -32,14 +32,6 @@ def pheno(
         dir_okay=False,
         resolve_path=True,
     ),
-    output: Path = typer.Option(
-        ...,
-        help="The directory where outputs should be created.",
-        exists=True,
-        file_okay=False,
-        dir_okay=True,
-        resolve_path=True,
-    ),
     name: str = typer.Option(
         ...,
         help="A descriptive name for the dataset the input belongs to. "
@@ -51,6 +43,18 @@ def pheno(
         callback=putil.validate_portal_uri,
         help="URL (HTTP/HTTPS) to a website or page that describes the dataset and access instructions (if available).",
     ),
+    output: Path = typer.Option(
+        default="pheno.jsonld",
+        help="The path for the output .jsonld file.",
+        file_okay=True,
+        dir_okay=False,
+        resolve_path=True,
+    ),
+    overwrite: bool = typer.Option(
+        False,
+        "--overwrite",
+        help="Overwrite output file if it already exists.",
+    ),
 ):
     """
     Process a tabular phenotypic file (.tsv) that has been successfully annotated
@@ -61,6 +65,9 @@ def pheno(
     graph datamodel for the provided phenotypic file in the .jsonld format.
     You can upload this .jsonld file to the Neurobagel graph.
     """
+    # Check if output file already exists
+    check_overwrite(output, overwrite)
+
     data_dictionary = load_json(dictionary)
     pheno_df = pd.read_csv(pheno, sep="\t", keep_default_na=False, dtype=str)
     putil.validate_inputs(data_dictionary, pheno_df)
@@ -140,11 +147,10 @@ def pheno(
     # TODO: we should revisit this because there may be reasons to have None be meaningful in the future
     context.update(**dataset.dict(exclude_none=True))
 
-    output_filename = output / "pheno.jsonld"
-    with open(output_filename, "w") as f:
+    with open(output, "w") as f:
         f.write(json.dumps(context, indent=2))
 
-    print(f"Saved output to:  {output_filename}")
+    print(f"Saved output to:  {output}")
 
 
 @bagel.command()
@@ -166,13 +172,17 @@ def bids(
         resolve_path=True,
     ),
     output: Path = typer.Option(
-        ...,
-        help="The directory where outputs should be created",
-        exists=True,
-        file_okay=False,
-        dir_okay=True,
+        help="The path for the output .jsonld file.",
+        default="pheno_bids.jsonld",
+        file_okay=True,
+        dir_okay=False,
         resolve_path=True,
     ),
+    overwrite: bool = typer.Option(
+        False,
+        "--overwrite",
+        help="Overwrite output file if it already exists.",
+    ),
 ):
     """
     Extract imaging metadata from a valid BIDS dataset and combine them
@@ -183,6 +193,9 @@ def bids(
     graph datamodel for the combined metadata in the .jsonld format.
     You can upload this .jsonld file to the Neurobagel graph.
     """
+    # Check if output file already exists
+    check_overwrite(output, overwrite)
+
     jsonld = load_json(jsonld_path)
     layout = BIDSLayout(bids_dir, validate=True)
 
@@ -264,8 +277,7 @@ def bids(
 
     merged_dataset = {**context, **pheno_dataset.dict(exclude_none=True)}
 
-    output_filename = output / "pheno_bids.jsonld"
-    with open(output_filename, "w") as f:
+    with open(output, "w") as f:
         f.write(json.dumps(merged_dataset, indent=2))
 
-    print(f"Saved output to:  {output_filename}")
+    print(f"Saved output to:  {output}")
diff --git a/bagel/tests/test_cli_bids.py b/bagel/tests/test_cli_bids.py
index b2534af..1812c0c 100644
--- a/bagel/tests/test_cli_bids.py
+++ b/bagel/tests/test_cli_bids.py
@@ -1,10 +1,21 @@
 from pathlib import Path
 
+import pytest
+
 from bagel.cli import bagel
 
 
+@pytest.fixture(scope="function")
+def default_pheno_bids_output_path(tmp_path):
+    "Return temporary bids command output filepath that uses the default filename."
+    return tmp_path / "pheno_bids.jsonld"
+
+
 def test_bids_valid_inputs_run_successfully(
-    runner, test_data_upload_path, bids_synthetic, tmp_path
+    runner,
+    test_data_upload_path,
+    bids_synthetic,
+    default_pheno_bids_output_path,
 ):
     """Basic smoke test for the "add-bids" subcommand"""
     result = runner.invoke(
@@ -16,12 +27,12 @@ def test_bids_valid_inputs_run_successfully(
             "--bids-dir",
             bids_synthetic,
             "--output",
-            tmp_path,
+            default_pheno_bids_output_path,
         ],
     )
     assert result.exit_code == 0, f"Errored out. STDOUT: {result.output}"
     assert (
-        tmp_path / "pheno_bids.jsonld"
+        default_pheno_bids_output_path
     ).exists(), "The pheno_bids.jsonld output was not created."
 
 
@@ -29,7 +40,7 @@ def test_bids_sessions_have_correct_labels(
     runner,
     test_data_upload_path,
     bids_synthetic,
-    tmp_path,
+    default_pheno_bids_output_path,
     load_test_json,
 ):
     """Check that sessions added to pheno_bids.jsonld have the expected labels."""
@@ -42,11 +53,11 @@ def test_bids_sessions_have_correct_labels(
             "--bids-dir",
             bids_synthetic,
             "--output",
-            tmp_path,
+            default_pheno_bids_output_path,
         ],
     )
 
-    pheno_bids = load_test_json(tmp_path / "pheno_bids.jsonld")
+    pheno_bids = load_test_json(default_pheno_bids_output_path)
     for sub in pheno_bids["hasSamples"]:
         assert ["ses-01", "ses-02"] == [
             ses["hasLabel"] for ses in sub["hasSession"]
@@ -56,7 +67,7 @@ def test_bids_sessions_have_correct_labels(
 def test_bids_data_with_sessions_have_correct_paths(
     runner,
     test_data_upload_path,
-    tmp_path,
+    default_pheno_bids_output_path,
     load_test_json,
 ):
     """
@@ -72,11 +83,11 @@ def test_bids_data_with_sessions_have_correct_paths(
             "--bids-dir",
             Path(__file__).parent / "../../bids-examples/synthetic",
             "--output",
-            tmp_path,
+            default_pheno_bids_output_path,
         ],
     )
 
-    pheno_bids = load_test_json(tmp_path / "pheno_bids.jsonld")
+    pheno_bids = load_test_json(default_pheno_bids_output_path)
     for sub in pheno_bids["hasSamples"]:
         for ses in sub["hasSession"]:
             assert sub["hasLabel"] in ses["hasFilePath"]
diff --git a/bagel/tests/test_cli_pheno.py b/bagel/tests/test_cli_pheno.py
index 8729e3d..76f811a 100644
--- a/bagel/tests/test_cli_pheno.py
+++ b/bagel/tests/test_cli_pheno.py
@@ -1,8 +1,16 @@
+import os
+
 import pytest
 
 from bagel.cli import bagel
 
 
+@pytest.fixture(scope="function")
+def default_pheno_output_path(tmp_path):
+    "Return temporary pheno command output filepath that uses the default filename."
+    return tmp_path / "pheno.jsonld"
+
+
 @pytest.mark.parametrize(
     "example",
     [
@@ -16,7 +24,11 @@
     ],
 )
 def test_pheno_valid_inputs_run_successfully(
-    runner, test_data, test_data_upload_path, tmp_path, example
+    runner,
+    test_data,
+    test_data_upload_path,
+    default_pheno_output_path,
+    example,
 ):
     """Basic smoke test for the "pheno" subcommand"""
     if example == "example_synthetic":
@@ -29,7 +41,7 @@ def test_pheno_valid_inputs_run_successfully(
                 "--dictionary",
                 test_data_upload_path / f"{example}.json",
                 "--output",
-                tmp_path,
+                default_pheno_output_path,
                 "--name",
                 "synthetic",
             ],
@@ -44,14 +56,14 @@ def test_pheno_valid_inputs_run_successfully(
                 "--dictionary",
                 test_data / f"{example}.json",
                 "--output",
-                tmp_path,
+                default_pheno_output_path,
                 "--name",
                 "do not care name",
             ],
         )
     assert result.exit_code == 0, f"Errored out. STDOUT: {result.output}"
     assert (
-        tmp_path / "pheno.jsonld"
+        default_pheno_output_path
     ).exists(), "The pheno.jsonld output was not created."
 
 
@@ -93,7 +105,12 @@ def test_pheno_valid_inputs_run_successfully(
     ],
 )
 def test_invalid_inputs_are_handled_gracefully(
-    runner, test_data, tmp_path, example, expected_exception, expected_message
+    runner,
+    test_data,
+    default_pheno_output_path,
+    example,
+    expected_exception,
+    expected_message,
 ):
     """Assures that we handle expected user errors in the input files gracefully"""
     with pytest.raises(expected_exception) as e:
@@ -106,7 +123,7 @@ def test_invalid_inputs_are_handled_gracefully(
                 "--dictionary",
                 test_data / f"{example}.json",
                 "--output",
-                tmp_path,
+                default_pheno_output_path,
                 "--name",
                 "do not care name",
             ],
@@ -129,7 +146,7 @@ def test_invalid_inputs_are_handled_gracefully(
 def test_invalid_portal_uris_produces_error(
     runner,
     test_data,
-    tmp_path,
+    default_pheno_output_path,
     portal,
 ):
     """Tests that invalid or non-HTTP/HTTPS URLs result in a user-friendly error."""
@@ -142,7 +159,7 @@ def test_invalid_portal_uris_produces_error(
             "--dictionary",
             test_data / "example2.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "test dataset 2",
             "--portal",
@@ -162,7 +179,7 @@ def test_invalid_portal_uris_produces_error(
 def test_missing_bids_levels_raises_warning(
     runner,
     test_data,
-    tmp_path,
+    default_pheno_output_path,
 ):
     with pytest.warns(UserWarning) as w:
         runner.invoke(
@@ -174,7 +191,7 @@ def test_missing_bids_levels_raises_warning(
                 "--dictionary",
                 test_data / "example12.json",
                 "--output",
-                tmp_path,
+                default_pheno_output_path,
                 "--name",
                 "testing dataset",
             ],
@@ -190,7 +207,7 @@ def test_missing_bids_levels_raises_warning(
 def test_bids_neurobagel_levels_mismatch_raises_warning(
     runner,
     test_data,
-    tmp_path,
+    default_pheno_output_path,
 ):
     with pytest.warns(UserWarning) as w:
         runner.invoke(
@@ -202,7 +219,7 @@ def test_bids_neurobagel_levels_mismatch_raises_warning(
                 "--dictionary",
                 test_data / "example13.json",
                 "--output",
-                tmp_path,
+                default_pheno_output_path,
                 "--name",
                 "testing dataset",
             ],
@@ -222,7 +239,7 @@ def test_bids_neurobagel_levels_mismatch_raises_warning(
 def test_unused_missing_values_raises_warning(
     runner,
     test_data,
-    tmp_path,
+    default_pheno_output_path,
 ):
     """
     Tests that an informative warning is raised when annotated missing values are not found in the
@@ -238,7 +255,7 @@ def test_unused_missing_values_raises_warning(
                 "--dictionary",
                 test_data / "example10.json",
                 "--output",
-                tmp_path,
+                default_pheno_output_path,
                 "--name",
                 "testing dataset",
             ],
@@ -256,7 +273,7 @@ def test_unused_missing_values_raises_warning(
 
 
 def test_that_output_file_contains_dataset_level_attributes(
-    runner, test_data, tmp_path, load_test_json
+    runner, test_data, default_pheno_output_path, load_test_json
 ):
     runner.invoke(
         bagel,
@@ -267,7 +284,7 @@ def test_that_output_file_contains_dataset_level_attributes(
             "--dictionary",
             test_data / "example2.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "my_dataset_name",
             "--portal",
@@ -275,14 +292,14 @@ def test_that_output_file_contains_dataset_level_attributes(
         ],
     )
 
-    pheno = load_test_json(tmp_path / "pheno.jsonld")
+    pheno = load_test_json(default_pheno_output_path)
 
     assert pheno.get("hasLabel") == "my_dataset_name"
     assert pheno.get("hasPortalURI") == "http://my_dataset_site.com"
 
 
 def test_diagnosis_and_control_status_handled(
-    runner, test_data, tmp_path, load_test_json
+    runner, test_data, default_pheno_output_path, load_test_json
 ):
     runner.invoke(
         bagel,
@@ -293,13 +310,13 @@ def test_diagnosis_and_control_status_handled(
             "--dictionary",
             test_data / "example6.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "my_dataset_name",
         ],
     )
 
-    pheno = load_test_json(tmp_path / "pheno.jsonld")
+    pheno = load_test_json(default_pheno_output_path)
 
     assert (
         pheno["hasSamples"][0]["hasDiagnosis"][0]["identifier"]
@@ -316,7 +333,11 @@ def test_diagnosis_and_control_status_handled(
     "attribute", ["hasSex", "hasDiagnosis", "hasAssessment", "isSubjectGroup"]
 )
 def test_controlled_terms_have_identifiers(
-    attribute, runner, test_data_upload_path, tmp_path, load_test_json
+    attribute,
+    runner,
+    test_data_upload_path,
+    default_pheno_output_path,
+    load_test_json,
 ):
     runner.invoke(
         bagel,
@@ -327,13 +348,13 @@ def test_controlled_terms_have_identifiers(
             "--dictionary",
             test_data_upload_path / "example_synthetic.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "do not care name",
         ],
     )
 
-    pheno = load_test_json(tmp_path / "pheno.jsonld")
+    pheno = load_test_json(default_pheno_output_path)
 
     for sub in pheno["hasSamples"]:
         if attribute in sub.keys():
@@ -346,7 +367,7 @@ def test_controlled_terms_have_identifiers(
 
 
 def test_controlled_term_classes_have_uri_type(
-    runner, test_data_upload_path, tmp_path, load_test_json
+    runner, test_data_upload_path, default_pheno_output_path, load_test_json
 ):
     """Tests that classes specified as schemaKeys (@type) for subject-level attributes in a .jsonld are also defined in the context."""
     runner.invoke(
@@ -358,7 +379,7 @@ def test_controlled_term_classes_have_uri_type(
             "--dictionary",
             test_data_upload_path / "example_synthetic.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "do not care name",
         ],
@@ -393,7 +414,12 @@ def test_controlled_term_classes_have_uri_type(
     ],
 )
 def test_assessment_data_are_parsed_correctly(
-    runner, test_data, tmp_path, load_test_json, assessment, subject
+    runner,
+    test_data,
+    default_pheno_output_path,
+    load_test_json,
+    assessment,
+    subject,
 ):
     runner.invoke(
         bagel,
@@ -404,13 +430,13 @@ def test_assessment_data_are_parsed_correctly(
             "--dictionary",
             test_data / "example6.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "my_dataset_name",
         ],
     )
 
-    pheno = load_test_json(tmp_path / "pheno.jsonld")
+    pheno = load_test_json(default_pheno_output_path)
 
     assert assessment == pheno["hasSamples"][subject].get("hasAssessment")
 
@@ -420,7 +446,12 @@ def test_assessment_data_are_parsed_correctly(
     [(20.5, 0), (pytest.approx(25.66, 0.01), 1)],
 )
 def test_cli_age_is_processed(
-    runner, test_data, tmp_path, load_test_json, expected_age, subject
+    runner,
+    test_data,
+    default_pheno_output_path,
+    load_test_json,
+    expected_age,
+    subject,
 ):
     runner.invoke(
         bagel,
@@ -431,18 +462,20 @@ def test_cli_age_is_processed(
             "--dictionary",
             test_data / "example2.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "my_dataset_name",
         ],
     )
 
-    pheno = load_test_json(tmp_path / "pheno.jsonld")
+    pheno = load_test_json(default_pheno_output_path)
 
     assert expected_age == pheno["hasSamples"][subject]["hasAge"]
 
 
-def test_output_includes_context(runner, test_data, tmp_path, load_test_json):
+def test_output_includes_context(
+    runner, test_data, default_pheno_output_path, load_test_json
+):
     runner.invoke(
         bagel,
         [
@@ -452,13 +485,13 @@ def test_output_includes_context(runner, test_data, tmp_path, load_test_json):
             "--dictionary",
             test_data / "example2.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "my_dataset_name",
         ],
     )
 
-    pheno = load_test_json(tmp_path / "pheno.jsonld")
+    pheno = load_test_json(default_pheno_output_path)
 
     assert pheno.get("@context") is not None
     assert all(
@@ -477,7 +510,7 @@ def test_output_includes_context(runner, test_data, tmp_path, load_test_json):
 def test_output_excludes_properties_for_missing_vals(
     runner,
     test_data_upload_path,
-    tmp_path,
+    default_pheno_output_path,
     load_test_json,
     sub_id,
     missing_val_property,
@@ -496,16 +529,81 @@ def test_output_excludes_properties_for_missing_vals(
             "--dictionary",
             test_data_upload_path / "example_synthetic.json",
             "--output",
-            tmp_path,
+            default_pheno_output_path,
             "--name",
             "BIDS synthetic test",
         ],
     )
 
-    pheno = load_test_json(tmp_path / "pheno.jsonld")
+    pheno = load_test_json(default_pheno_output_path)
     for sub in pheno["hasSamples"]:
         if sub["hasLabel"] == sub_id:
             for entry in missing_val_property:
                 assert (
                     sub.get(entry) is None
                 ), f"{sub_id} output contains value for {entry} where annotated as missing"
+
+
+def test_default_output_filename(runner, test_data_upload_path, tmp_path):
+    """Tests that the default output filename is used correctly when --output is not set."""
+    os.chdir(tmp_path)
+
+    runner.invoke(
+        bagel,
+        [
+            "pheno",
+            "--pheno",
+            test_data_upload_path / "example_synthetic.tsv",
+            "--dictionary",
+            test_data_upload_path / "example_synthetic.json",
+            "--name",
+            "BIDS synthetic test",
+        ],
+    )
+
+    assert (tmp_path / "pheno.jsonld").exists()
+
+
+@pytest.mark.parametrize(
+    "overwrite_flag, expected_stdout",
+    [
+        ([], "already exists"),
+        (["--overwrite"], "Saved output to"),
+    ],
+)
+def test_overwrite_flag_behaviour(
+    runner, test_data_upload_path, tmp_path, overwrite_flag, expected_stdout
+):
+    """Tests that an existing output file is only overwritten if --overwrite is used."""
+    runner.invoke(
+        bagel,
+        [
+            "pheno",
+            "--pheno",
+            test_data_upload_path / "example_synthetic.tsv",
+            "--dictionary",
+            test_data_upload_path / "example_synthetic.json",
+            "--name",
+            "BIDS synthetic test",
+            "--output",
+            tmp_path / "synthetic_dataset.jsonld",
+        ],
+    )
+
+    overwrite_result = runner.invoke(
+        bagel,
+        [
+            "pheno",
+            "--pheno",
+            test_data_upload_path / "example_synthetic.tsv",
+            "--dictionary",
+            test_data_upload_path / "example_synthetic.json",
+            "--name",
+            "BIDS synthetic test",
+            "--output",
+            tmp_path / "synthetic_dataset.jsonld",
+        ]
+        + overwrite_flag,
+    )
+
+    assert expected_stdout in overwrite_result.output
diff --git a/bagel/utility.py b/bagel/utility.py
index a7f33cb..71d0a97 100644
--- a/bagel/utility.py
+++ b/bagel/utility.py
@@ -1,8 +1,21 @@
 import json
 from pathlib import Path
 
+import typer
+
 
 def load_json(input_p: Path) -> dict:
     """Load a user-specified json type file."""
     with open(input_p, "r") as f:
         return json.load(f)
+
+
+def check_overwrite(output: Path, overwrite: bool):
+    """Exit program gracefully if an output file already exists but --overwrite has not been set."""
+    if output.exists() and not overwrite:
+        raise typer.Exit(
+            typer.style(
+                f"Output file {output} already exists. Use --overwrite to overwrite.",
+                fg=typer.colors.RED,
+            )
+        )
diff --git a/neurobagel_examples b/neurobagel_examples
index 63dc797..05ab0bd 160000
--- a/neurobagel_examples
+++ b/neurobagel_examples
@@ -1 +1 @@
-Subproject commit 63dc797f8c717bdde7ae94db5f8b0d59e79fba7d
+Subproject commit 05ab0bdfee095f2e25797a57f26943eeaff248ec