diff --git a/pycytominer/cyto_utils/collate.py b/pycytominer/cyto_utils/collate.py
index 4d51b249..6dcc282f 100644
--- a/pycytominer/cyto_utils/collate.py
+++ b/pycytominer/cyto_utils/collate.py
@@ -3,6 +3,7 @@
 import subprocess
 import sys
 import sqlite3
+import warnings
 
 
 def run_check_errors(cmd):
@@ -81,6 +82,17 @@ def collate(
             """
         )
 
+    # show a warning about collate deprecation
+    warnings.warn(
+        (
+            "With the deprecation of cytominer-database",
+            "pycytominer.cyto_utils.collate will be removed in future versions of Pycytominer. "
+            "Please consider using CellProfiler's ExportToDatabase module to create single-cell "
+            "SQLite files or CytoTable to create single-cell Parquet files.",
+        ),
+        DeprecationWarning,
+    )
+
     # Set up directories (these need to be abspaths to keep from confusing makedirs later)
     input_dir = pathlib.Path(f"{base_directory}/analysis/{batch}/{plate}/{csv_dir}")
     backend_dir = pathlib.Path(f"{base_directory}/backend/{batch}/{plate}")
diff --git a/pyproject.toml b/pyproject.toml
index 327378f6..ae05d1d9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -175,6 +175,9 @@ lint.per-file-ignores."tests/*" = [ "S101" ]
 
 [tool.pytest.ini_options]
 testpaths = "tests"
+filterwarnings = [
+  "ignore::DeprecationWarning:pycytominer.*",
+]
 
 [tool.mypy]
 exclude = [