diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1b44e98f..1a53e1fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 - `email` and `additionalContacts` in API reference json schema (#380)
 ### Changed
 - Updated versions of external actions and MongoDB in GitHub workflows (#374)
+- Allow updating contact's email and href separately using the command line (#381)
 ### Fixed
 - Fixed typo on conda installation docs (#373)
 
diff --git a/patientMatcher/cli/add.py b/patientMatcher/cli/add.py
index 69d1bafa..cce3fb09 100644
--- a/patientMatcher/cli/add.py
+++ b/patientMatcher/cli/add.py
@@ -4,6 +4,7 @@
 
 import click
 from flask.cli import current_app, with_appcontext
+
 from patientMatcher.resources import path_to_benchmark_patients
 from patientMatcher.utils.add import add_node, load_demo_patients
 from patientMatcher.utils.delete import drop_all_collections
diff --git a/patientMatcher/cli/commands.py b/patientMatcher/cli/commands.py
index cd99610f..f5e54f91 100644
--- a/patientMatcher/cli/commands.py
+++ b/patientMatcher/cli/commands.py
@@ -6,6 +6,7 @@
 from flask import Flask, current_app
 from flask.cli import FlaskGroup, routes_command, run_command, with_appcontext
 from flask_mail import Message
+
 from patientMatcher import __version__
 from patientMatcher.server import create_app
 
diff --git a/patientMatcher/cli/remove.py b/patientMatcher/cli/remove.py
index 7be55c6c..e2908de3 100644
--- a/patientMatcher/cli/remove.py
+++ b/patientMatcher/cli/remove.py
@@ -3,6 +3,7 @@
 
 import click
 from flask.cli import current_app, with_appcontext
+
 from patientMatcher.utils.delete import delete_by_query
 
 
diff --git a/patientMatcher/cli/update.py b/patientMatcher/cli/update.py
index 28e7a02c..e49ae719 100644
--- a/patientMatcher/cli/update.py
+++ b/patientMatcher/cli/update.py
@@ -4,11 +4,13 @@
 
 import click
 from flask.cli import current_app, with_appcontext
+
 from patientMatcher.parse.patient import EMAIL_REGEX, href_validate
 from patientMatcher.utils.patient import patients
 from patientMatcher.utils.update import update_resources
 
 LOG = logging.getLogger(__name__)
+HREF_FIELD = "contact.href"
 
 
 @click.group()
@@ -19,54 +21,69 @@ def update():
 
 @update.command()
 @with_appcontext
-@click.option(
-    "-o", "--old-href", type=click.STRING, nargs=1, required=True, help="Old contact href"
-)
-@click.option("-h", "--href", type=click.STRING, nargs=1, required=True, help="New contact href")
-@click.option("-n", "--name", type=click.STRING, nargs=1, required=True, help="New contact name")
-@click.option(
-    "--institution", type=click.STRING, nargs=1, required=False, help="New contact institution"
-)
-def contact(old_href, href, name, institution):
-    """Update contact person for a group of patients"""
-
-    # If new contact is a simple email, add "mailto" schema
-    if bool(EMAIL_REGEX.match(href)) is True and "mailto:" not in href:
-        href = ":".join(["mailto", href])
-
-    if href_validate(href) is False:
-        LOG.error(
-            "Provided href does not have a valid schema. Provide either a URL (http://.., https://..) or an email address (mailto:..)"
+@click.option("--href", type=click.STRING, required=False, help="Contact's href")
+@click.option("--email", type=click.STRING, required=False, help="Contact's email")
+@click.option("--new-href", type=click.STRING, required=False, help="New href")
+@click.option("--new-email", type=click.STRING, required=False, help="New email")
+@click.option("--new-name", type=click.STRING, required=False, help="New name")
+@click.option("--new-institution", type=click.STRING, required=False, help="New institution")
+def contact(href, email, new_href, new_email, new_name, new_institution):
+    """Update contact person for a group of patients."""
+
+    # Validate exactly one identifier
+    if bool(href) == bool(email):
+        raise click.UsageError("You must provide EITHER --href or --email")
+
+    # Validate at least one field to update
+    if not any([new_href, new_email, new_name, new_institution]):
+        click.echo(
+            "Provide at least a field you wish to update: "
+            "--new-href / --new-email / --new-name / --new-institution"
         )
         return
 
-    database = current_app.db
-    query = {"contact.href": {"$regex": old_href}}
+    # Build query
+    query = {HREF_FIELD: {"$regex": href}} if href else {"contact.email": email}
 
-    # Retrieving all patients matching the given old_href
-    old_contact_patients = patients(database=database, match_query=query)
-    # Retriving unique contacts for the above patients
-    match_contacts = list(old_contact_patients.distinct("contact.href"))
+    database = current_app.db
+    matching_patients = patients(database=database, match_query=query)
+    matching_contacts = list(matching_patients.distinct(HREF_FIELD))
 
-    if len(match_contacts) == 0:
-        click.echo(f"No patients found with contact URI '{old_href}'")
+    if not matching_contacts:
+        click.echo(f"No patients found with query '{query}'")
         return
-    if len(match_contacts) > 1:
+    if len(matching_contacts) > 1:
         click.echo(
-            f"Your search for contact url '{old_href}' is returning more than one patients' contact: {match_contacts}.\nPlease restrict your search by typing a different href."
+            f"Your search for contact query '{query}' is returning more than one patients' contact.\n"
+            "Please restrict your search by typing a different href/email."
         )
         return
-    # Search is returning only one contact, it's OK to use it for updating patients
-    matches = list(old_contact_patients)
-    new_contact = dict(href=href, name=name)
-    if institution:
-        new_contact["institution"] = institution
 
+    # Build update dict
+    set_options = {}
+    if new_href:
+        if EMAIL_REGEX.match(new_href) and not new_href.startswith("mailto:"):
+            new_href = f"mailto:{new_href}"
+        if not href_validate(new_href):
+            LOG.error(
+                "Provided href does not have a valid schema. Provide either a URL (http://.., https://..) or an email address (mailto:..)"
+            )
+            return
+        set_options[HREF_FIELD] = new_href
+    if new_email:
+        set_options["contact.email"] = new_email
+    if new_name:
+        set_options["contact.name"] = new_name
+    if new_institution:
+        set_options["contact.institution"] = new_institution
+
+    # Confirm and update
+    patient_count = len(list(matching_patients))
     if click.confirm(
-        f"{len(matches)} patients with the old contact href '{matches[0]['contact']['href']}' will be updated with contact info:{new_contact}. Confirm?",
+        f"{patient_count} patients will be updated with contact info: {set_options}. Confirm?",
         abort=True,
     ):
-        result = database.patients.update_many(query, {"$set": {"contact": new_contact}})
+        result = database.patients.update_many(query, {"$set": set_options})
         click.echo(f"Contact information was updated for {result.modified_count} patients.")
 
 
diff --git a/patientMatcher/match/handler.py b/patientMatcher/match/handler.py
index 6d7c2689..5ed2b3fe 100644
--- a/patientMatcher/match/handler.py
+++ b/patientMatcher/match/handler.py
@@ -5,10 +5,11 @@
 import logging
 
 import requests
+from werkzeug.datastructures import Headers
+
 from patientMatcher.match.genotype_matcher import match as genomatch
 from patientMatcher.match.phenotype_matcher import match as phenomatch
 from patientMatcher.parse.patient import json_patient
-from werkzeug.datastructures import Headers
 
 LOG = logging.getLogger(__name__)
 
diff --git a/patientMatcher/parse/patient.py b/patientMatcher/parse/patient.py
index 9052e548..0593f0c9 100644
--- a/patientMatcher/parse/patient.py
+++ b/patientMatcher/parse/patient.py
@@ -7,6 +7,7 @@
 from urllib.parse import urlparse
 
 from jsonschema import FormatChecker, RefResolver, validate
+
 from patientMatcher.utils.gene import ensembl_to_symbol, entrez_to_symbol, symbol_to_ensembl
 from patientMatcher.utils.variant import liftover
 
diff --git a/patientMatcher/server/__init__.py b/patientMatcher/server/__init__.py
index 177e7166..0b4a4fb4 100644
--- a/patientMatcher/server/__init__.py
+++ b/patientMatcher/server/__init__.py
@@ -8,11 +8,7 @@
 from flask import Flask
 from flask_mail import Mail
 from pymongo import MongoClient
-from pymongo.errors import (
-    ConnectionFailure,
-    OperationFailure,
-    ServerSelectionTimeoutError,
-)
+from pymongo.errors import ConnectionFailure, OperationFailure, ServerSelectionTimeoutError
 
 from patientMatcher.resources import path_to_hpo_terms, path_to_phenotype_annotations
 from patientMatcher.utils.notify import TlsSMTPHandler, admins_email_format
diff --git a/patientMatcher/server/controllers.py b/patientMatcher/server/controllers.py
index ced963f2..f0c0a6c0 100644
--- a/patientMatcher/server/controllers.py
+++ b/patientMatcher/server/controllers.py
@@ -3,6 +3,7 @@
 
 from flask import current_app, jsonify
 from jsonschema import ValidationError
+
 from patientMatcher.__version__ import __version__
 from patientMatcher.auth.auth import authorize
 from patientMatcher.constants import STATUS_CODES
diff --git a/patientMatcher/server/views.py b/patientMatcher/server/views.py
index 3c53dbe0..a24dc4ae 100644
--- a/patientMatcher/server/views.py
+++ b/patientMatcher/server/views.py
@@ -6,6 +6,7 @@
 from bson import json_util
 from flask import Blueprint, current_app, jsonify, render_template, request, send_from_directory
 from flask_negotiate import consumes, produces
+
 from patientMatcher.auth.auth import authorize
 from patientMatcher.match.handler import internal_matcher, patient_matches
 from patientMatcher.utils.add import backend_add_patient
diff --git a/patientMatcher/utils/add.py b/patientMatcher/utils/add.py
index 145cce64..43d8b042 100644
--- a/patientMatcher/utils/add.py
+++ b/patientMatcher/utils/add.py
@@ -5,9 +5,10 @@
 import sys
 
 import enlighten
+from pymongo import MongoClient
+
 from patientMatcher.match.handler import external_matcher
 from patientMatcher.parse.patient import mme_patient
-from pymongo import MongoClient
 
 LOG = logging.getLogger(__name__)
 
diff --git a/patientMatcher/utils/notify.py b/patientMatcher/utils/notify.py
index d90f227f..b081b055 100644
--- a/patientMatcher/utils/notify.py
+++ b/patientMatcher/utils/notify.py
@@ -4,6 +4,7 @@
 from logging.handlers import SMTPHandler
 
 from flask_mail import Message
+
 from patientMatcher.__version__ import __version__
 
 LOG = logging.getLogger(__name__)
diff --git a/patientMatcher/utils/patient.py b/patientMatcher/utils/patient.py
index 454ce34a..866d58b6 100644
--- a/patientMatcher/utils/patient.py
+++ b/patientMatcher/utils/patient.py
@@ -50,10 +50,7 @@ def patients(database, ids=None, match_query=None):
     if ids:  # if only specified patients should be returned
         query["_id"] = {"$in": ids}
     elif match_query:
-        LOG.info("Return patients matching query {}".format(match_query))
         query = match_query
-    else:
-        LOG.info("Return all patients in database")
 
     results = database["patients"].find(query)
     return results
diff --git a/patientMatcher/utils/update.py b/patientMatcher/utils/update.py
index 2a4a2534..74ca7fc3 100644
--- a/patientMatcher/utils/update.py
+++ b/patientMatcher/utils/update.py
@@ -3,6 +3,7 @@
 
 import requests
 from clint.textui import progress
+
 from patientMatcher.constants import PHENOTYPE_TERMS
 
 LOG = logging.getLogger(__name__)
diff --git a/tests/backend/test_backend_patient.py b/tests/backend/test_backend_patient.py
index d1c58245..a8e13b6c 100644
--- a/tests/backend/test_backend_patient.py
+++ b/tests/backend/test_backend_patient.py
@@ -3,6 +3,7 @@
 import os
 
 import pytest
+
 from patientMatcher.parse.patient import mme_patient
 from patientMatcher.utils.add import backend_add_patient, load_demo_patients
 from patientMatcher.utils.delete import delete_by_query
diff --git a/tests/cli/test_commands.py b/tests/cli/test_commands.py
index d7abda9e..5d258206 100644
--- a/tests/cli/test_commands.py
+++ b/tests/cli/test_commands.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 from flask_mail import Message
+
 from patientMatcher.cli.commands import cli
 
 
diff --git a/tests/cli/test_update.py b/tests/cli/test_update.py
index 66e039d4..8cfa3c32 100644
--- a/tests/cli/test_update.py
+++ b/tests/cli/test_update.py
@@ -1,8 +1,11 @@
 import responses
+
 from patientMatcher.cli.commands import cli
 from patientMatcher.constants import PHENOTYPE_TERMS
 
 CONTACT_HREF = "contact.href"
+NEW_HREF = "https://test.com"
+NEW_EMAIL = "new.email@mail.com"
 NEW_NAME = "New Name"
 TEST_INST = "Test Institution"
 
@@ -34,115 +37,175 @@ def test_update_resources(mock_app):
     assert result.exit_code == 0
 
 
-def test_update_contact(mock_app, gpx4_patients):
-    """Test the command to bulk-update patients contact"""
+def test_update_contact_success(mock_app, gpx4_patients, monkeypatch):
+    """Test updating a contact successfully"""
 
     runner = mock_app.test_cli_runner()
     patients_collection = mock_app.db.patients
 
-    # GIVEN a database with some patients
+    # GIVEN a database with patients
     patients_collection.insert_many(gpx4_patients)
-    test_patients = patients_collection.find()
-    # Sharing a contact information
-    contacts = test_patients.distinct(CONTACT_HREF)
+    contacts = list(patients_collection.find().distinct(CONTACT_HREF))
     assert len(contacts) == 1
 
-    # WHEN their contact info is updated using the cli
-    new_href = "new.contact@mail.com"
+    # Mock click.confirm to always return True
+    monkeypatch.setattr("click.confirm", lambda *args, **kwargs: True)
+
+    # WHEN updating contact info
     result = runner.invoke(
         cli,
         [
             "update",
             "contact",
-            "--old-href",
-            contacts[0],
             "--href",
-            new_href,
-            "--name",
+            contacts[0],
+            "--new-href",
+            NEW_HREF,
+            "--new-email",
+            NEW_EMAIL,
+            "--new-name",
             NEW_NAME,
-            "--institution",
+            "--new-institution",
             TEST_INST,
         ],
-        input="y",
     )
+
+    # THEN the update should succeed
     assert result.exit_code == 0
+    assert "Contact information was updated" in result.output
+
+    updated_patient = list(patients_collection.find({CONTACT_HREF: NEW_HREF}))
+    assert len(updated_patient) > 0
+    assert updated_patient[0]["contact"]["href"] == NEW_HREF
+    assert updated_patient[0]["contact"]["email"] == NEW_EMAIL
+    assert updated_patient[0]["contact"]["name"] == NEW_NAME
+    assert updated_patient[0]["contact"]["institution"] == TEST_INST
 
-    # THEN the config info should be updated
-    updated_patient = patients_collection.find({CONTACT_HREF: ":".join(["mailto", new_href])})
-    assert len(list(updated_patient)) > 0
+
+def test_update_contact_validation(mock_app, gpx4_patients):
+    """Test validations for contact CLI"""
+
+    runner = mock_app.test_cli_runner()
+    patients_collection = mock_app.db.patients
+
+    patients_collection.insert_many(gpx4_patients)
+    contacts = list(patients_collection.find().distinct(CONTACT_HREF))
+    assert len(contacts) == 1
+
+    # WHEN no update fields are provided
+    result_no_update = runner.invoke(
+        cli,
+        ["update", "contact", "--href", contacts[0]],
+    )
+    assert result_no_update.exit_code == 0
+    assert "Provide at least a field you wish to update" in result_no_update.output
+
+    # WHEN both --href and --email are provided
+    result_invalid = runner.invoke(
+        cli,
+        [
+            "update",
+            "contact",
+            "--href",
+            contacts[0],
+            "--email",
+            "some@email.com",
+            "--new-name",
+            "Name",
+        ],
+    )
+    assert result_invalid.exit_code != 0
+    assert "You must provide EITHER --href or --email" in result_invalid.output
 
 
 def test_update_contact_no_href_match(mock_app, gpx4_patients):
-    """Test the command to bulk-update patients contact when old contact href is not matching any patients"""
+    """
+    Test the command when the provided old contact href does not match any patients.
+    The command should not update anything and should output a message.
+    """
 
     runner = mock_app.test_cli_runner()
     patients_collection = mock_app.db.patients
 
     # GIVEN a database with some patients
     patients_collection.insert_many(gpx4_patients)
-    test_patients = patients_collection.find()
-    # Sharing a contact information
-    contacts = test_patients.distinct(CONTACT_HREF)
+    contacts = list(patients_collection.find().distinct(CONTACT_HREF))
     assert len(contacts) == 1
-    old_contact_href = contacts[0]
+    existing_href = contacts[0]
 
-    # GIVEN a contact href without matches in the patients documents
-    wrong_href = "some_href"
-    assert wrong_href not in old_contact_href
+    # GIVEN a contact href that doesn't exist in the database
+    wrong_href = "nonexistent_href"
+    assert wrong_href not in existing_href
 
-    # WHEN their contact info is updated using the cli
+    # WHEN attempting to update using the CLI
     new_href = "new.contact@mail.com"
     result = runner.invoke(
         cli,
         [
             "update",
             "contact",
-            "--old-href",
-            wrong_href,
             "--href",
+            wrong_href,
+            "--new-href",
             new_href,
-            "--name",
+            "--new-name",
             NEW_NAME,
-            "--institution",
+            "--new-institution",
             TEST_INST,
         ],
+        input="y",  # in case the CLI asks for confirmation
     )
+
+    # THEN the CLI should succeed but print a message about no patients found
     assert result.exit_code == 0
+    assert "No patients found with query" in result.output
 
-    # THEN no patients contact should be updated
-    assert patients_collection.find_one({CONTACT_HREF: ":".join(["mailto", new_href])}) is None
+    # AND no patient contact should be updated
+    updated_patient = patients_collection.find_one({CONTACT_HREF: f"mailto:{new_href}"})
+    assert updated_patient is None
 
 
 def test_update_contact_multiple_href_match(mock_app, gpx4_patients):
-    """Test the command to bulk-update patients contact when old contact href is matching more than one patient contact"""
+    """
+    Test the command when the old contact href matches multiple patients.
+    The CLI should print a warning and not update any patient contact.
+    """
 
     runner = mock_app.test_cli_runner()
     patients_collection = mock_app.db.patients
 
-    assert len(gpx4_patients) == 2
-    # GIVEN a database with 2 patients with sligthly different contact href
+    assert len(gpx4_patients) >= 2
+
+    # GIVEN a database with 2 patients sharing similar href patterns
     gpx4_patients[0]["contact"]["href"] = "test_1@mail.com"
-    gpx4_patients[0]["contact"]["href"] = "test_2@mail.com"
+    gpx4_patients[1]["contact"]["href"] = "test_2@mail.com"
     patients_collection.insert_many(gpx4_patients)
 
-    # WHEN their contact info is updated using the cli but the search for the old href returns multiple contacts
-    old_href = "test_"
+    # WHEN attempting to update with a href pattern that matches multiple contacts
+    old_href_pattern = "test_"  # this will match both test_1 and test_2
     new_href = "test_3@mail.com"
+
     result = runner.invoke(
         cli,
         [
             "update",
             "contact",
-            "--old-href",
-            old_href,
             "--href",
+            old_href_pattern,
+            "--new-href",
             new_href,
-            "--name",
+            "--new-name",
             NEW_NAME,
-            "--institution",
+            "--new-institution",
             TEST_INST,
         ],
+        input="y",
     )
 
-    # THEN no patients contact should be updated
-    assert patients_collection.find_one({CONTACT_HREF: ":".join(["mailto", new_href])}) is None
+    # THEN the CLI should print a warning about multiple matches
+    assert result.exit_code == 0
+    assert "returning more than one patients' contact" in result.output
+
+    # AND no patient should be updated
+    updated_patient = patients_collection.find_one({CONTACT_HREF: f"mailto:{new_href}"})
+    assert updated_patient is None
diff --git a/tests/conftest.py b/tests/conftest.py
index 78869331..5d65b011 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -4,6 +4,7 @@
 import mongomock
 import pytest
 import responses
+
 from patientMatcher.resources import path_to_benchmark_patients
 from patientMatcher.server import create_app
 
diff --git a/tests/match/test_GT_matching.py b/tests/match/test_GT_matching.py
index 6c8cd302..cb24b7bb 100644
--- a/tests/match/test_GT_matching.py
+++ b/tests/match/test_GT_matching.py
@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import responses
+
 from patientMatcher.match.genotype_matcher import match
 from patientMatcher.parse.patient import mme_patient
 
diff --git a/tests/match/test_matching_handler.py b/tests/match/test_matching_handler.py
index f2fdfa94..1541d27a 100644
--- a/tests/match/test_matching_handler.py
+++ b/tests/match/test_matching_handler.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 import requests
 import responses
+
 from patientMatcher.match.handler import external_matcher, internal_matcher
 from patientMatcher.parse.patient import mme_patient
 from patientMatcher.utils.add import backend_add_patient
diff --git a/tests/server/test_server_responses.py b/tests/server/test_server_responses.py
index 02bc3500..098ab9a1 100644
--- a/tests/server/test_server_responses.py
+++ b/tests/server/test_server_responses.py
@@ -2,6 +2,7 @@
 import json
 
 import responses
+
 from patientMatcher.__version__ import __version__
 from patientMatcher.match.handler import patient_matches
 from patientMatcher.parse.patient import mme_patient
diff --git a/tests/utils/test_ensembl_rest_api.py b/tests/utils/test_ensembl_rest_api.py
index 0fe31d0d..4bf9d9ad 100644
--- a/tests/utils/test_ensembl_rest_api.py
+++ b/tests/utils/test_ensembl_rest_api.py
@@ -1,9 +1,10 @@
 # -*- coding: UTF-8 -*-
 import pytest
 import responses
-from patientMatcher.utils import ensembl_rest_client as ensembl_api
 from requests.exceptions import MissingSchema
 
+from patientMatcher.utils import ensembl_rest_client as ensembl_api
+
 
 @responses.activate
 def test_except_on_invalid_response():
diff --git a/tests/utils/test_gene.py b/tests/utils/test_gene.py
index 7fc8761b..007be56e 100644
--- a/tests/utils/test_gene.py
+++ b/tests/utils/test_gene.py
@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import responses
+
 from patientMatcher.utils.ensembl_rest_client import requests
 from patientMatcher.utils.gene import ensembl_to_symbol, entrez_to_symbol, symbol_to_ensembl
 
diff --git a/tests/utils/test_variant.py b/tests/utils/test_variant.py
index 938c752b..2a844197 100644
--- a/tests/utils/test_variant.py
+++ b/tests/utils/test_variant.py
@@ -1,4 +1,5 @@
 import responses
+
 from patientMatcher.utils.variant import liftover