diff --git a/mypy/join.py b/mypy/join.py
index fcfc6cbaa0e7..65cc3bef66a4 100644
--- a/mypy/join.py
+++ b/mypy/join.py
@@ -8,7 +8,7 @@
 import mypy.typeops
 from mypy.expandtype import expand_type
 from mypy.maptype import map_instance_to_supertype
-from mypy.nodes import CONTRAVARIANT, COVARIANT, INVARIANT, VARIANCE_NOT_READY
+from mypy.nodes import CONTRAVARIANT, COVARIANT, INVARIANT, VARIANCE_NOT_READY, TypeInfo
 from mypy.state import state
 from mypy.subtypes import (
     SubtypeContext,
@@ -168,9 +168,20 @@ def join_instances_via_supertype(self, t: Instance, s: Instance) -> ProperType:
         # Compute the "best" supertype of t when joined with s.
         # The definition of "best" may evolve; for now it is the one with
         # the longest MRO.  Ties are broken by using the earlier base.
-        best: ProperType | None = None
+
+        # Go over both sets of bases in case there's an explicit Protocol base. This is important
+        # to ensure commutativity of join (although in cases where both classes have relevant
+        # Protocol bases this maybe might still not be commutative)
+        base_types: dict[TypeInfo, None] = {}  # dict to deduplicate but preserve order
         for base in t.type.bases:
-            mapped = map_instance_to_supertype(t, base.type)
+            base_types[base.type] = None
+        for base in s.type.bases:
+            if base.type.is_protocol and is_subtype(t, base):
+                base_types[base.type] = None
+
+        best: ProperType | None = None
+        for base_type in base_types:
+            mapped = map_instance_to_supertype(t, base_type)
             res = self.join_instances(mapped, s)
             if best is None or is_better(res, best):
                 best = res
@@ -662,6 +673,10 @@ def is_better(t: Type, s: Type) -> bool:
     if isinstance(t, Instance):
         if not isinstance(s, Instance):
             return True
+        if t.type.is_protocol != s.type.is_protocol:
+            if t.type.fullname != "builtins.object" and s.type.fullname != "builtins.object":
+                # mro of protocol is not really relevant
+                return not t.type.is_protocol
         # Use len(mro) as a proxy for the better choice.
         if len(t.type.mro) > len(s.type.mro):
             return True
diff --git a/test-data/unit/check-inference.test b/test-data/unit/check-inference.test
index 381f73ed9862..4cf24ef9cb6c 100644
--- a/test-data/unit/check-inference.test
+++ b/test-data/unit/check-inference.test
@@ -3888,6 +3888,53 @@ def a4(x: List[str], y: List[Never]) -> None:
     z1[1].append("asdf")  # E: "object" has no attribute "append"
 [builtins fixtures/dict.pyi]
 
+
+[case testDeterminismCommutativityWithJoinInvolvingProtocolBaseAndPromotableType]
+# flags: --python-version 3.11
+# Regression test for https://github.com/python/mypy/issues/16979#issuecomment-1982246306
+from __future__ import annotations
+
+from typing import Any, Generic, Protocol, TypeVar, overload, cast
+from typing_extensions import Never
+
+T = TypeVar("T")
+U = TypeVar("U")
+
+class _SupportsCompare(Protocol):
+    def __lt__(self, other: Any, /) -> bool:
+        return True
+
+class Comparable(_SupportsCompare):
+    pass
+
+comparable: Comparable = Comparable()
+
+from typing import _promote
+
+class floatlike:
+    def __lt__(self, other: floatlike, /) -> bool: ...
+
+@_promote(floatlike)
+class intlike:
+    def __lt__(self, other: intlike, /) -> bool: ...
+
+
+class A(Generic[T, U]):
+    @overload
+    def __init__(self: A[T, T], a: T, b: T, /) -> None: ...  # type: ignore[overload-overlap]
+    @overload
+    def __init__(self: A[T, U], a: T, b: U, /) -> Never: ...
+    def __init__(self, *a) -> None: ...
+
+def join(a: T, b: T) -> T: ...
+
+reveal_type(join(intlike(), comparable))  # N: Revealed type is "__main__._SupportsCompare"
+reveal_type(join(comparable, intlike()))  # N: Revealed type is "__main__._SupportsCompare"
+reveal_type(A(intlike(), comparable))  # N: Revealed type is "__main__.A[__main__._SupportsCompare, __main__._SupportsCompare]"
+reveal_type(A(comparable, intlike()))  # N: Revealed type is "__main__.A[__main__._SupportsCompare, __main__._SupportsCompare]"
+[builtins fixtures/tuple.pyi]
+[typing fixtures/typing-medium.pyi]
+
 [case testTupleJoinFallbackInference]
 foo = [
     (1, ("a", "b")),
diff --git a/test-data/unit/check-protocols.test b/test-data/unit/check-protocols.test
index 5e34d5223907..934f48a5e9c3 100644
--- a/test-data/unit/check-protocols.test
+++ b/test-data/unit/check-protocols.test
@@ -4461,6 +4461,30 @@ f2(a4)  # E: Argument 1 to "f2" has incompatible type "A4"; expected "P2" \
         # N:     foo: expected setter type "C1", got "str"
 [builtins fixtures/property.pyi]
 
+
+[case testExplicitProtocolJoinPreference]
+from typing import Protocol, TypeVar
+
+T = TypeVar("T")
+
+class Proto1(Protocol):
+    def foo(self) -> int: ...
+class Proto2(Proto1):
+    def bar(self) -> str: ...
+class Proto3(Proto2):
+    def baz(self) -> str: ...
+
+class Base: ...
+
+class A(Base, Proto3): ...
+class B(Base, Proto3): ...
+
+def join(a: T, b: T) -> T: ...
+
+def main(a: A, b: B) -> None:
+    reveal_type(join(a, b))  # N: Revealed type is "__main__.Proto3"
+    reveal_type(join(b, a))  # N: Revealed type is "__main__.Proto3"
+
 [case testProtocolImplementationWithDescriptors]
 from typing import Any, Protocol