diff --git a/qiskit/utils/__init__.py b/qiskit/utils/__init__.py
index a0992fa2745c..3aa70917c1ac 100644
--- a/qiskit/utils/__init__.py
+++ b/qiskit/utils/__init__.py
@@ -58,7 +58,6 @@
 """
 
 from .quantum_instance import QuantumInstance
-from .deprecation import _filter_deprecation_warnings
 from .deprecation import deprecate_arguments
 from .deprecation import deprecate_function
 from .multiprocessing import local_hardware_info
diff --git a/qiskit/utils/deprecation.py b/qiskit/utils/deprecation.py
index 14938bc88dbf..1a73803ab4f3 100644
--- a/qiskit/utils/deprecation.py
+++ b/qiskit/utils/deprecation.py
@@ -13,44 +13,9 @@
 """Deprecation utilities"""
 
 import functools
-import re
 import warnings
 
 
-def _filter_deprecation_warnings():
-    """Apply filters to deprecation warnings.
-
-    Force the `DeprecationWarning` warnings to be displayed for the qiskit
-    module, overriding the system configuration as they are ignored by default
-    [1] for end-users. Additionally, silence the `ChangedInMarshmallow3Warning`
-    messages.
-
-    TODO: on Python 3.7, this might not be needed due to PEP-0565 [2].
-
-    [1] https://docs.python.org/3/library/warnings.html#default-warning-filters
-    [2] https://www.python.org/dev/peps/pep-0565/
-    """
-    deprecation_filter = (
-        "default",
-        None,
-        DeprecationWarning,
-        re.compile(r"^qiskit\.*", re.UNICODE),
-        0,
-    )
-
-    # Instead of using warnings.simple_filter() directly, the internal
-    # _add_filter() function is used for being able to match against the
-    # module.
-    try:
-        warnings._add_filter(*deprecation_filter, append=False)
-    except AttributeError:
-        # ._add_filter is internal and not available in some Python versions.
-        pass
-
-
-_filter_deprecation_warnings()
-
-
 def deprecate_arguments(kwarg_map):
     """Decorator to automatically alias deprecated argument names and warn upon use."""
 
@@ -80,13 +45,9 @@ def deprecate_function(msg, stacklevel=2):
     def decorator(func):
         @functools.wraps(func)
         def wrapper(*args, **kwargs):
-            # warn only once
-            if not wrapper._warned:
-                warnings.warn(msg, DeprecationWarning, stacklevel=stacklevel)
-                wrapper._warned = True
+            warnings.warn(msg, DeprecationWarning, stacklevel=stacklevel)
             return func(*args, **kwargs)
 
-        wrapper._warned = False
         return wrapper
 
     return decorator
diff --git a/releasenotes/notes/remove-manual-warning-filters-028646b73bb86860.yaml b/releasenotes/notes/remove-manual-warning-filters-028646b73bb86860.yaml
new file mode 100644
index 000000000000..eb25d1a20336
--- /dev/null
+++ b/releasenotes/notes/remove-manual-warning-filters-028646b73bb86860.yaml
@@ -0,0 +1,11 @@
+---
+upgrade:
+  - |
+    An internal filter override that caused all Qiskit deprecation warnings to be displayed has been removed.
+    This means that the behaviour will now revert to the standard Python behaviour for deprecations; you should only see a ``DeprecationWarning`` if it was triggered by code in the main script file, interpreter session or Jupyter notebook.
+    The user will no longer be blamed with a warning if internal Qiskit functions call deprecated behaviour.
+    If you write libraries, you should occasionally run with the default warning filters disabled, or have tests which always run with them disabled.
+  - |
+    Certain warnings used to be only issued once, even if triggered from multiple places.
+    This behaviour has been removed, so it is possible that if you call deprecated functions, you may see more warnings than you did before.
+    You should change any deprecated function calls to the suggested versions, because the deprecated forms will be removed in future Qiskit releases.