diff --git a/capellambse/loader/core.py b/capellambse/loader/core.py
index 85a68fd8..4fe28621 100644
--- a/capellambse/loader/core.py
+++ b/capellambse/loader/core.py
@@ -36,6 +36,11 @@
 from capellambse.loader import exs
 from capellambse.loader.modelinfo import ModelInfo
 
+if sys.version_info >= (3, 13):
+    from warnings import deprecated
+else:
+    from typing_extensions import deprecated
+
 E = builder.ElementMaker()
 LOGGER = logging.getLogger(__name__)
 PROJECT_NATURE = "org.polarsys.capella.project.nature"
@@ -401,6 +406,10 @@ def __replace_nsmap(self, new_nsmap: dict[str | None, str]) -> None:
 
         self.root = new_root
 
+    @deprecated(
+        "iterall_xt() is deprecated,"
+        " use iterall() or iter_qtypes() + iter_qtype() instead"
+    )
     def iterall_xt(
         self, xtypes: cabc.Container[str]
     ) -> cabc.Iterator[etree._Element]:
diff --git a/capellambse/model/__init__.py b/capellambse/model/__init__.py
index 257bb01e..5d9cf186 100644
--- a/capellambse/model/__init__.py
+++ b/capellambse/model/__init__.py
@@ -7,9 +7,15 @@
 import collections.abc as cabc
 import enum
 import functools
+import sys
 import typing as t
 import warnings
 
+if sys.version_info >= (3, 13):
+    from warnings import deprecated
+else:
+    from typing_extensions import deprecated
+
 VIRTUAL_NAMESPACE_PREFIX = (
     "https://dsd-dbs.github.io/py-capellambse/virtual-namespace/"
 )
@@ -34,6 +40,7 @@
 """Covariant TypeVar (unbound)."""
 
 
+@deprecated("set_accessor is deprecated and no longer needed")
 def set_accessor(
     cls: type[ModelObject], attr: str, accessor: Accessor
 ) -> None:
@@ -41,11 +48,16 @@ def set_accessor(
     accessor.__set_name__(cls, attr)
 
 
+@deprecated("set_self_references is deprecated, use a 'Containment' instead")
 def set_self_references(*args: tuple[type[ModelObject], str]) -> None:
     for cls, attr in args:
-        setattr(cls, attr, DirectProxyAccessor(cls, aslist=ElementList))
+        setattr(cls, attr, DirectProxyAccessor(cls, aslist=ElementList))  # type: ignore[deprecated]
 
 
+@deprecated(
+    '`@attr_equal("...")` is deprecated,'
+    ' use `class X(ModelElement, eq="...")` instead'
+)
 def attr_equal(attr: str) -> cabc.Callable[[type[T]], type[T]]:
     def add_wrapped_eq(cls: type[T]) -> type[T]:
         orig_eq = cls.__eq__
diff --git a/capellambse/model/_descriptors.py b/capellambse/model/_descriptors.py
index a671664c..db6de21d 100644
--- a/capellambse/model/_descriptors.py
+++ b/capellambse/model/_descriptors.py
@@ -40,6 +40,7 @@
 import itertools
 import logging
 import operator
+import sys
 import types
 import typing as t
 import warnings
@@ -53,6 +54,11 @@
 
 from . import T, T_co, U_co
 
+if sys.version_info >= (3, 13):
+    from warnings import deprecated
+else:
+    from typing_extensions import deprecated
+
 _NotSpecifiedType = t.NewType("_NotSpecifiedType", object)
 _NOT_SPECIFIED = _NotSpecifiedType(object())
 "Used to detect unspecified optional arguments"
@@ -60,6 +66,7 @@
 LOGGER = logging.getLogger(__name__)
 
 
+@deprecated("@xtype_handler is deprecated and no longer used")
 def xtype_handler(
     arch: str | None = None, /, *xtypes: str
 ) -> cabc.Callable[[type[T]], type[T]]:
@@ -72,6 +79,7 @@ def xtype_handler(
     return lambda i: i
 
 
+@deprecated("build_xtype is deprecated")
 def build_xtype(class_: type[_obj.ModelObject]) -> str:
     ns: _obj.Namespace | None = getattr(class_, "__capella_namespace__", None)
     if ns is None:
@@ -581,6 +589,7 @@ def _resolve_super_attributes(
             self.single_attr = super_acc.single_attr
 
 
+@deprecated("WritableAccessor is deprecated, use Relation instead")
 class WritableAccessor(Accessor["_obj.ElementList[T_co]"], t.Generic[T_co]):
     """An Accessor that also provides write support on lists it returns."""
 
@@ -814,6 +823,7 @@ def purge_references(self, obj, target):
         )
 
 
+@deprecated("PhysicalAccessor is deprecated, use Relation instead")
 class PhysicalAccessor(Accessor["_obj.ElementList[T_co]"], t.Generic[T_co]):
     """Helper super class for accessors that work with real elements."""
 
@@ -847,18 +857,19 @@ def __init__(
         super().__init__()
         if xtypes is None:
             self.xtypes = (
-                {build_xtype(class_)}
+                {build_xtype(class_)}  # type: ignore[deprecated]
                 if class_ is not _obj.ModelElement
                 else set()
             )
         elif isinstance(xtypes, type):
             assert issubclass(xtypes, _obj.ModelElement)
-            self.xtypes = {build_xtype(xtypes)}
+            self.xtypes = {build_xtype(xtypes)}  # type: ignore[deprecated]
         elif isinstance(xtypes, str):
             self.xtypes = {xtypes}
         else:
             self.xtypes = {
-                i if isinstance(i, str) else build_xtype(i) for i in xtypes
+                i if isinstance(i, str) else build_xtype(i)  # type: ignore[deprecated]
+                for i in xtypes
             }
 
         self.aslist = aslist
@@ -894,6 +905,7 @@ def _make_list(self, parent_obj, elements):
         )
 
 
+@deprecated("DirectProxyAccessor is deprecated, use Containment instead")
 class DirectProxyAccessor(WritableAccessor[T_co], PhysicalAccessor[T_co]):
     """Creates proxy objects on the fly."""
 
@@ -986,10 +998,11 @@ def __init__(
         elif isinstance(rootelem, type) and issubclass(
             rootelem, _obj.ModelElement
         ):
-            self.rootelem = [build_xtype(rootelem)]
+            self.rootelem = [build_xtype(rootelem)]  # type: ignore[deprecated]
         else:
             self.rootelem = [
-                i if isinstance(i, str) else build_xtype(i) for i in rootelem
+                i if isinstance(i, str) else build_xtype(i)  # type: ignore[deprecated]
+                for i in rootelem
             ]
 
     def __get__(self, obj, objtype=None):
@@ -1158,6 +1171,9 @@ def purge_references(
         yield
 
 
+@deprecated(
+    "DeepProxyAccessor is deprecated, use @property and model.search() instead"
+)
 class DeepProxyAccessor(PhysicalAccessor[T_co]):
     """A DirectProxyAccessor that searches recursively through the tree."""
 
@@ -1207,9 +1223,9 @@ def __init__(
         elif isinstance(rootelem, type) and issubclass(
             rootelem, _obj.ModelElement
         ):
-            self.rootelem = (build_xtype(rootelem),)
+            self.rootelem = (build_xtype(rootelem),)  # type: ignore[deprecated]
         elif not isinstance(rootelem, str):  # type: ignore[unreachable]
-            self.rootelem = tuple(build_xtype(i) for i in rootelem)
+            self.rootelem = tuple(build_xtype(i) for i in rootelem)  # type: ignore[deprecated]
         else:
             raise TypeError(
                 "Invalid 'rootelem', expected a type or list of types: "
@@ -1262,6 +1278,10 @@ class Allocation(Relationship[T_co]):
     backattr: str | None
 
     @t.overload
+    @deprecated(
+        "Raw classes, xsi:type strings and 'aslist' are deprecated,"
+        " migrate to (Namespace, 'ClassName') tuples and drop aslist=..."
+    )
     def __init__(
         self,
         tag: str | None,
@@ -1921,6 +1941,10 @@ def _resolve_super_attributes(
         self.attr = super_acc.attr
 
 
+@deprecated(
+    "PhysicalLinkEndsAccessor is deprecated,"
+    " use Association with fixed_length=2 instead"
+)
 class PhysicalLinkEndsAccessor(Association[T_co]):
     def __init__(
         self,
@@ -2035,6 +2059,9 @@ def __get__(self, obj, objtype=None):
         return _obj.wrap_xml(obj._model, parent)
 
 
+@deprecated(
+    "AttributeMatcherAccessor is deprecated, use FilterAccessor instead"
+)
 class AttributeMatcherAccessor(DirectProxyAccessor[T_co]):
     __slots__ = (
         "_AttributeMatcherAccessor__aslist",
@@ -2462,6 +2489,11 @@ def purge_references(
                 yield
 
 
+@deprecated(
+    "TypecastAccessor is deprecated,"
+    " use Filter to perform filtering"
+    " or Alias to create an unfiltered Alias"
+)
 class TypecastAccessor(WritableAccessor[T_co], PhysicalAccessor[T_co]):
     """Changes the static type of the value of another accessor.
 
@@ -2545,7 +2577,7 @@ def create(
         if typehint:
             raise TypeError(f"{self._qualname} does not support type hints")
         acc: WritableAccessor = getattr(self.class_, self.attr)
-        obj = acc.create(elmlist, build_xtype(self.class_), **kw)
+        obj = acc.create(elmlist, build_xtype(self.class_), **kw)  # type: ignore[deprecated]
         assert isinstance(obj, self.class_)
         return obj
 
@@ -2584,9 +2616,14 @@ def purge_references(
 class Containment(Relationship[T_co]):
     __slots__ = ("classes", "role_tag")
 
+    aslist: type[_obj.ElementListCouplingMixin]
     alternate: type[_obj.ModelObject] | None
 
     @t.overload
+    @deprecated(
+        "Raw classes, xsi:type strings and 'aslist' are deprecated,"
+        " migrate to (Namespace, 'ClassName') tuples and drop aslist=..."
+    )
     def __init__(
         self,
         role_tag: str,
diff --git a/capellambse/model/_obj.py b/capellambse/model/_obj.py
index de965a12..902807a0 100644
--- a/capellambse/model/_obj.py
+++ b/capellambse/model/_obj.py
@@ -38,6 +38,7 @@
 import logging
 import operator
 import re
+import sys
 import textwrap
 import typing as t
 import warnings
@@ -52,6 +53,11 @@
 
 from . import VIRTUAL_NAMESPACE_PREFIX, T, U, _descriptors, _pods, _styleclass
 
+if sys.version_info >= (3, 13):
+    from warnings import deprecated
+else:
+    from typing_extensions import deprecated
+
 if t.TYPE_CHECKING:
     import capellambse.metamodel as mm
 
@@ -598,6 +604,7 @@ def progress_status(self) -> str:
         return wrap_xml(self._model, self._model._loader[uuid]).name
 
     @classmethod
+    @deprecated("ModelElement.from_model is deprecated, use wrap_xml instead")
     def from_model(
         cls, model: capellambse.MelodyModel, element: etree._Element
     ) -> te.Self:
@@ -1603,6 +1610,7 @@ def _newlist(self, elements: list[etree._Element]) -> ElementList[T]:
         return newlist
 
 
+@deprecated("MixedElementList is deprecated, use base ElementList instead")
 class MixedElementList(ElementList[ModelElement]):
     """ElementList that handles proxies using ``XTYPE_HANDLERS``."""
 
@@ -2038,6 +2046,10 @@ def wrap_xml(
     return obj
 
 
+@deprecated(
+    "find_wrapper is deprecated,"
+    " use resolve_class_name or MelodyModel.resolve_class instead"
+)
 @functools.cache
 def find_wrapper(typehint: str) -> tuple[type[ModelObject], ...]:
     """Find the possible wrapper classes for the hinted type.