diff --git a/pydatalab/schemas/cell.json b/pydatalab/schemas/cell.json
index a41903da4..94cd46694 100644
--- a/pydatalab/schemas/cell.json
+++ b/pydatalab/schemas/cell.json
@@ -48,6 +48,10 @@
         "$ref": "#/definitions/Person"
       }
     },
+    "deleted": {
+      "title": "Deleted",
+      "type": "boolean"
+    },
     "type": {
       "title": "Type",
       "default": "cells",
diff --git a/pydatalab/schemas/equipment.json b/pydatalab/schemas/equipment.json
index d5bd7eeb1..2ece5d99b 100644
--- a/pydatalab/schemas/equipment.json
+++ b/pydatalab/schemas/equipment.json
@@ -48,6 +48,10 @@
         "$ref": "#/definitions/Person"
       }
     },
+    "deleted": {
+      "title": "Deleted",
+      "type": "boolean"
+    },
     "type": {
       "title": "Type",
       "default": "equipment",
diff --git a/pydatalab/schemas/sample.json b/pydatalab/schemas/sample.json
index 35cb3fc64..ee38292ad 100644
--- a/pydatalab/schemas/sample.json
+++ b/pydatalab/schemas/sample.json
@@ -48,6 +48,10 @@
         "$ref": "#/definitions/Person"
       }
     },
+    "deleted": {
+      "title": "Deleted",
+      "type": "boolean"
+    },
     "type": {
       "title": "Type",
       "default": "samples",
diff --git a/pydatalab/schemas/startingmaterial.json b/pydatalab/schemas/startingmaterial.json
index ad1446b3a..c3034bb7b 100644
--- a/pydatalab/schemas/startingmaterial.json
+++ b/pydatalab/schemas/startingmaterial.json
@@ -48,6 +48,10 @@
         "$ref": "#/definitions/Person"
       }
     },
+    "deleted": {
+      "title": "Deleted",
+      "type": "boolean"
+    },
     "type": {
       "title": "Type",
       "default": "starting_materials",
diff --git a/pydatalab/src/pydatalab/models/items.py b/pydatalab/src/pydatalab/models/items.py
index 4195f1ce6..21c76d22d 100644
--- a/pydatalab/src/pydatalab/models/items.py
+++ b/pydatalab/src/pydatalab/models/items.py
@@ -10,6 +10,7 @@
     HasOwner,
     HasRevisionControl,
     IsCollectable,
+    IsDeletable,
 )
 from pydatalab.models.utils import (
     HumanReadableIdentifier,
@@ -19,7 +20,7 @@
 )
 
 
-class Item(Entry, HasOwner, HasRevisionControl, IsCollectable, HasBlocks, abc.ABC):
+class Item(Entry, IsDeletable, HasOwner, HasRevisionControl, IsCollectable, HasBlocks, abc.ABC):
     """The generic model for data types that will be exposed with their own named endpoints."""
 
     refcode: Refcode = None  # type: ignore
diff --git a/pydatalab/src/pydatalab/models/traits.py b/pydatalab/src/pydatalab/models/traits.py
index 07be0d937..2cf34fa6d 100644
--- a/pydatalab/src/pydatalab/models/traits.py
+++ b/pydatalab/src/pydatalab/models/traits.py
@@ -78,3 +78,18 @@ def add_missing_collection_relationships(cls, values):
             raise RuntimeError("Relationships and collections mismatch")
 
         return values
+
+
+class IsDeletable(BaseModel):
+    """Adds a 'private' trait for whether the item is deleted.
+    This can be used to soft-delete entries in the database.
+    """
+
+    deleted: bool = Field(None)
+
+    @root_validator(pre=True)
+    def check_deleted(cls, values):
+        """If `deleted` is set to anything but `True`, drop the field."""
+        if "deleted" in values and values["deleted"] is not True:
+            values.pop("deleted")
+        return values
diff --git a/pydatalab/src/pydatalab/mongo.py b/pydatalab/src/pydatalab/mongo.py
index d0195a97f..d9b12c8aa 100644
--- a/pydatalab/src/pydatalab/mongo.py
+++ b/pydatalab/src/pydatalab/mongo.py
@@ -6,6 +6,7 @@
 from pydantic import BaseModel
 from pymongo.errors import ConnectionFailure
 
+from pydatalab.logger import LOGGER
 from pydatalab.models import ITEM_MODELS
 
 __all__ = (
@@ -95,6 +96,7 @@ def check_mongo_connection() -> None:
 def create_default_indices(
     client: Optional[pymongo.MongoClient] = None,
     background: bool = False,
+    allow_rebuild: bool = False,
 ) -> List[str]:
     """Creates indices for the configured or passed MongoClient.
 
@@ -105,7 +107,10 @@ def create_default_indices(
         - A text index over user names and identities.
 
     Parameters:
+        client: The MongoClient to use. If None, a new one will be created.
         background: If true, indexes will be created as background jobs.
+        allow_rebuild: If true, named indexes will be recreated if they already exist
+            with alternative options.
 
     Returns:
         A list of messages returned by each `create_index` call.
@@ -146,14 +151,30 @@ def create_fts():
         weights={"collection_id": 3, "title": 3, "description": 3},
     )
 
-    ret += db.items.create_index("type", name="item type", background=background)
-    ret += db.items.create_index(
-        "item_id", unique=True, name="unique item ID", background=background
-    )
-    ret += db.items.create_index(
-        "refcode", unique=True, name="unique refcode", background=background
-    )
-    ret += db.items.create_index("last_modified", name="last modified", background=background)
+    indices = [
+        {"type": {"name": "item type", "background": background}},
+        {
+            "item_id": {
+                "name": "unique item ID",
+                "unique": True,
+                "background": background,
+                "partialFilterExpression": {"deleted": {"$eq": None}},
+            }
+        },
+        {"refcode": {"name": "unique refcode", "unique": True, "background": background}},
+        {"last_modified": {"name": "last modified", "background": background}},
+        {"creator_ids": {"name": "creators", "background": background}},
+        {"deleted": {"name": "deleted items", "background": background}},
+    ]
+
+    for index in indices:
+        for field, options in index.items():
+            try:
+                ret += db.items.create_index(field, **options)
+            except pymongo.errors.OperationFailure as exc:
+                LOGGER.warning("Rebuilding index %s", options["name"], exc_info=exc)
+                db.items.drop_index(options["name"])
+                ret += db.items.create_index(field, **options)
 
     user_fts_fields = {"identities.name", "display_name"}
 
diff --git a/pydatalab/src/pydatalab/permissions.py b/pydatalab/src/pydatalab/permissions.py
index c36e3a0eb..729d2ee8c 100644
--- a/pydatalab/src/pydatalab/permissions.py
+++ b/pydatalab/src/pydatalab/permissions.py
@@ -60,7 +60,7 @@ def wrapped_route(*args, **kwargs):
     return wrapped_route
 
 
-def get_default_permissions(user_only: bool = True) -> Dict[str, Any]:
+def get_default_permissions(user_only: bool = True, match_deleted: bool = False) -> Dict[str, Any]:
     """Return the MongoDB query terms corresponding to the current user.
 
     Will return open permissions if a) the `CONFIG.TESTING` parameter is `True`,
@@ -70,11 +70,17 @@ def get_default_permissions(user_only: bool = True) -> Dict[str, Any]:
         user_only: Whether to exclude items that also have no attached user (`False`),
             i.e., public items. This should be set to `False` when reading (and wanting
             to return public items), but left as `True` when modifying or removing items.
+        match_deleted: Whether to include items that have been soft-deleted.
 
     """
 
+    return_match: dict = {"$and": []}
+
+    if not match_deleted:
+        return_match["$and"].append({"deleted": {"$ne": True}})
+
     if CONFIG.TESTING:
-        return {}
+        return return_match
 
     if (
         current_user.is_authenticated
@@ -109,11 +115,16 @@ def get_default_permissions(user_only: bool = True) -> Dict[str, Any]:
             # TODO: remove this hack when permissions are refactored. Currently starting_materials and equipment
             # are a special case that should be group editable, so even when the route has asked to only edit this
             # user's stuff, we can also let starting materials and equipment through.
-            user_perm = {"$or": [user_perm, {"type": {"$in": ["starting_materials", "equipment"]}}]}
-            return user_perm
-        return {"$or": [user_perm, null_perm]}
+            return_match["$and"].append(
+                {"$or": [user_perm, {"type": {"$in": ["starting_materials", "equipment"]}}]}
+            )
+            return return_match
+
+        return_match["$and"].append({"$or": [user_perm, null_perm]})
+        return return_match
 
     elif user_only:
         return {"_id": -1}
 
-    return null_perm
+    return_match["$and"].append(null_perm)
+    return return_match
diff --git a/pydatalab/src/pydatalab/routes/v0_1/graphs.py b/pydatalab/src/pydatalab/routes/v0_1/graphs.py
index 82c3d122c..82c618041 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/graphs.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/graphs.py
@@ -31,7 +31,7 @@ def get_graph_cy_format(item_id: Optional[str] = None, collection_id: Optional[s
             query = {}
         all_documents = flask_mongo.db.items.find(
             {**query, **get_default_permissions(user_only=False)},
-            projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
+            projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1, "deleted": 1},
         )
         node_ids: Set[str] = {document["item_id"] for document in all_documents}
         all_documents.rewind()
@@ -43,7 +43,7 @@ def get_graph_cy_format(item_id: Optional[str] = None, collection_id: Optional[s
                     "$or": [{"item_id": item_id}, {"relationships.item_id": item_id}],
                     **get_default_permissions(user_only=False),
                 },
-                projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
+                projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1, "deleted": 1},
             )
         )
 
@@ -59,7 +59,7 @@ def get_graph_cy_format(item_id: Optional[str] = None, collection_id: Optional[s
                     "$or": or_query,
                     **get_default_permissions(user_only=False),
                 },
-                projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
+                projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1, "deleted": 1},
             )
 
             all_documents.extend(next_shell)
@@ -71,9 +71,14 @@ def get_graph_cy_format(item_id: Optional[str] = None, collection_id: Optional[s
     # Collect the elements that have already been added to the graph, to avoid duplication
     drawn_elements = set()
     node_collections = set()
+    deleted_items = set()
     for document in all_documents:
         # for some reason, document["relationships"] is sometimes equal to None, so we
         # need this `or` statement.
+        if document.get("deleted", None):
+            deleted_items.add(document["item_id"])
+            continue
+
         for relationship in document.get("relationships") or []:
             # only considering child-parent relationships
             if relationship.get("type") == "collections" and not collection_id:
@@ -124,6 +129,8 @@ def get_graph_cy_format(item_id: Optional[str] = None, collection_id: Optional[s
             source = relationship["item_id"]
             if source not in node_ids:
                 continue
+            if target not in node_ids:
+                continue
             edge_id = f"{source}->{target}"
             if edge_id not in drawn_elements:
                 drawn_elements.add(edge_id)
@@ -151,6 +158,14 @@ def get_graph_cy_format(item_id: Optional[str] = None, collection_id: Optional[s
                 }
             )
 
+    # Filter out any edges to deleted nodes
+    edges_to_remove = []
+    for ind, edge in enumerate(edges):
+        if edge["data"]["source"] in deleted_items or edge["data"]["target"] in deleted_items:
+            edges_to_remove.append(edge["data"]["id"])
+
+    edges = [edge for edge in edges if edge["data"]["id"] not in edges_to_remove]
+
     # We want to filter out all the starting materials that don't have relationships since there are so many of them:
     whitelist = {edge["data"]["source"] for edge in edges}
 
diff --git a/pydatalab/src/pydatalab/routes/v0_1/items.py b/pydatalab/src/pydatalab/routes/v0_1/items.py
index 60628e021..95f951aff 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/items.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/items.py
@@ -288,6 +288,7 @@ def search_items():
         nresults: Maximum number of  (default 100)
         types: If None, search all types of items. Otherwise, a list of strings
                giving the types to consider. (e.g. ["samples","starting_materials"])
+        match_deleted: Whether to include items that have been soft-deleted.
 
     Returns:
         response list of dictionaries containing the matching items in order of
@@ -297,13 +298,14 @@ def search_items():
     query = request.args.get("query", type=str)
     nresults = request.args.get("nresults", default=100, type=int)
     types = request.args.get("types", default=None)
+    match_deleted = request.args.get("match_deleted", default=False, type=bool)
     if isinstance(types, str):
         # should figure out how to parse as list automatically
         types = types.split(",")
 
     match_obj = {
         "$text": {"$search": query},
-        **get_default_permissions(user_only=False),
+        **get_default_permissions(user_only=False, match_deleted=match_deleted),
     }
     if types is not None:
         match_obj["type"] = {"$in": types}
@@ -467,7 +469,7 @@ def _create_sample(
         )
 
     # check to make sure that item_id isn't taken already
-    if flask_mongo.db.items.find_one({"item_id": sample_dict["item_id"]}):
+    if flask_mongo.db.items.find_one({"item_id": sample_dict["item_id"], "deleted": {"$ne": True}}):
         return (
             dict(
                 status="error",
@@ -697,21 +699,46 @@ def update_item_permissions(refcode: str):
     return jsonify({"status": "success"}), 200
 
 
+@ITEMS.route("/items/<refcode>", methods=["DELETE"])
 @ITEMS.route("/delete-sample/", methods=["POST"])
-def delete_sample():
-    request_json = request.get_json()  # noqa: F821 pylint: disable=undefined-variable
-    item_id = request_json["item_id"]
+def delete_sample(refcode: str | None = None, item_id: str | None = None):
+    """Sets the `deleted` status an item with the given refcode."""
 
-    result = flask_mongo.db.items.delete_one(
-        {"item_id": item_id, **get_default_permissions(user_only=True)}
+    if refcode is None:
+        request_json = request.get_json()  # noqa: F821 pylint: disable=undefined-variable
+        item_id = request_json["item_id"]
+
+    if item_id:
+        match = {"item_id": item_id}
+    elif refcode:
+        if not len(refcode.split(":")) == 2:
+            refcode = f"{CONFIG.IDENTIFIER_PREFIX}:{refcode}"
+
+        match = {"refcode": refcode}
+    else:
+        return (
+            jsonify(
+                {
+                    "status": "error",
+                    "message": "No item_id or refcode provided.",
+                }
+            ),
+            400,
+        )
+
+    LOGGER.warning(f"Setting deleted status for {refcode=}, {item_id=}.")
+
+    result = flask_mongo.db.items.update_one(
+        {**match, **get_default_permissions(user_only=True)},
+        {"$set": {"deleted": True}},
     )
 
-    if result.deleted_count != 1:
+    if result.modified_count != 1:
         return (
             jsonify(
                 {
                     "status": "error",
-                    "message": f"Authorization required to attempt to delete sample with {item_id=} from the database.",
+                    "message": f"Authorization required to attempt to delete sample with {refcode=} / {item_id=} from the database.",
                 }
             ),
             401,
@@ -734,6 +761,8 @@ def get_item_data(
     """Generates a JSON response for the item with the given `item_id`,
     or `refcode` additionally resolving relationships to files and other items.
 
+    Will return deleted items if specifically requested.
+
     Parameters:
        load_blocks: Whether to regenerate any data blocks associated with this
            sample (i.e., create the Python object corresponding to the block and
@@ -768,9 +797,10 @@ def get_item_data(
             {
                 "$match": {
                     **match,
-                    **get_default_permissions(user_only=False),
+                    **get_default_permissions(user_only=False, match_deleted=True),
                 }
             },
+            {"$sort": {"deleted": 1}},
             {"$lookup": creators_lookup()},
             {"$lookup": collections_lookup()},
             {"$lookup": files_lookup()},
@@ -874,9 +904,14 @@ def get_item_data(
         f["immutable_id"]: f for f in return_dict.get("files") or []
     }
 
+    warnings = []
+    if return_dict.get("deleted"):
+        warnings += [f"The item with refcode {return_dict['refcode']!r} has been deleted."]
+
     return jsonify(
         {
             "status": "success",
+            "warnings": warnings,
             "item_id": item_id,
             "item_data": return_dict,
             "files_data": files_data,
diff --git a/pydatalab/tests/server/test_equipment.py b/pydatalab/tests/server/test_equipment.py
index 093113b8f..01afabe65 100644
--- a/pydatalab/tests/server/test_equipment.py
+++ b/pydatalab/tests/server/test_equipment.py
@@ -124,4 +124,5 @@ def test_delete_equipment(admin_client, default_equipment_dict):
     response = admin_client.get(
         f"/get-item-data/{default_equipment_dict['item_id']}",
     )
-    assert response.status_code == 404
+    assert response.status_code == 200
+    assert "has been deleted" in response.json["warnings"][0]
diff --git a/pydatalab/tests/server/test_samples.py b/pydatalab/tests/server/test_samples.py
index 69b438d47..cc0ea8c46 100644
--- a/pydatalab/tests/server/test_samples.py
+++ b/pydatalab/tests/server/test_samples.py
@@ -134,7 +134,29 @@ def test_delete_sample(client, default_sample_dict):
     response = client.get(
         f"/get-item-data/{default_sample_dict['item_id']}",
     )
-    assert response.status_code == 404
+    assert response.status_code == 200
+    assert "has been deleted" in response.json["warnings"][0]
+
+    # Check that the ID is freed up, and that delete by refcode also works
+    response = client.post("/new-sample/", json=default_sample_dict)
+    # Test that 201: Created is emitted
+    assert response.status_code == 201, response.json
+    assert response.json["status"] == "success"
+
+    response = client.get(
+        f"/get-item-data/{default_sample_dict['item_id']}",
+    )
+    refcode = response.json["item_data"]["refcode"]
+
+    del_response = client.delete(
+        f"/items/{refcode}",
+    )
+    assert del_response.status_code == 200
+    assert del_response.json["status"] == "success"
+
+    response = client.get(f"/items/{refcode}")
+    assert response.status_code == 200
+    assert f"The item with refcode {refcode!r} has been deleted." == response.json["warnings"][0]
 
 
 @pytest.mark.dependency(depends=["test_delete_sample"])
@@ -146,7 +168,16 @@ def test_create_indices(real_mongo_client):
 
     create_default_indices(real_mongo_client)
     indexes = list(real_mongo_client.get_database().items.list_indexes())
-    expected_index_names = ("_id_", "items full-text search", "item type", "unique item ID")
+    expected_index_names = (
+        "_id_",
+        "items full-text search",
+        "item type",
+        "unique item ID",
+        "unique refcode",
+        "last modified",
+        "creators",
+        "deleted items",
+    )
     names = [index["name"] for index in indexes]
 
     assert all(name in names for name in expected_index_names)
diff --git a/pydatalab/tests/server/test_starting_materials.py b/pydatalab/tests/server/test_starting_materials.py
index ff9761c44..6e897c581 100644
--- a/pydatalab/tests/server/test_starting_materials.py
+++ b/pydatalab/tests/server/test_starting_materials.py
@@ -127,6 +127,7 @@ def test_delete_starting_material(admin_client, default_starting_material_dict):
     )
     assert response.status_code == 200
     assert response.json["status"] == "success"
+    assert "has been deleted" in response.json["warnings"][0]
 
     # Check it was actually deleted
     response = admin_client.get(