diff --git a/src/v/pandaproxy/schema_registry/sharded_store.cc b/src/v/pandaproxy/schema_registry/sharded_store.cc
index 7d2192b5ea96..67e15dc180a1 100644
--- a/src/v/pandaproxy/schema_registry/sharded_store.cc
+++ b/src/v/pandaproxy/schema_registry/sharded_store.cc
@@ -519,11 +519,12 @@ ss::future<bool> sharded_store::set_compatibility(
       });
 }
 
-ss::future<bool> sharded_store::clear_compatibility(subject sub) {
+ss::future<bool>
+sharded_store::clear_compatibility(seq_marker marker, subject sub) {
     auto sub_shard{shard_for(sub)};
     co_return co_await _store.invoke_on(
-      sub_shard, _smp_opts, [sub{std::move(sub)}](store& s) {
-          return s.clear_compatibility(sub).value();
+      sub_shard, _smp_opts, [marker, sub{std::move(sub)}](store& s) {
+          return s.clear_compatibility(marker, sub).value();
       });
 }
 
diff --git a/src/v/pandaproxy/schema_registry/sharded_store.h b/src/v/pandaproxy/schema_registry/sharded_store.h
index 6802365aed74..c6473f0e6bc6 100644
--- a/src/v/pandaproxy/schema_registry/sharded_store.h
+++ b/src/v/pandaproxy/schema_registry/sharded_store.h
@@ -131,7 +131,7 @@ class sharded_store {
       seq_marker marker, subject sub, compatibility_level compatibility);
 
     ///\brief Clear the compatibility level for a subject.
-    ss::future<bool> clear_compatibility(subject sub);
+    ss::future<bool> clear_compatibility(seq_marker marker, subject sub);
 
     ///\brief Check if the provided schema is compatible with the subject and
     /// version, according the the current compatibility.
diff --git a/src/v/pandaproxy/schema_registry/storage.h b/src/v/pandaproxy/schema_registry/storage.h
index 38aa1121930d..ff831df9778a 100644
--- a/src/v/pandaproxy/schema_registry/storage.h
+++ b/src/v/pandaproxy/schema_registry/storage.h
@@ -1287,7 +1287,13 @@ struct consume_to_store {
         try {
             vlog(plog.debug, "Applying: {}", key);
             if (!val) {
-                co_await _store.clear_compatibility(*key.sub);
+                co_await _store.clear_compatibility(
+                  seq_marker{
+                    .seq = key.seq,
+                    .node = key.node,
+                    .version{invalid_schema_version}, // Not applicable
+                    .key_type = seq_marker_key_type::config},
+                  *key.sub);
             } else if (key.sub) {
                 co_await _store.set_compatibility(
                   seq_marker{
diff --git a/src/v/pandaproxy/schema_registry/store.h b/src/v/pandaproxy/schema_registry/store.h
index 700c45aee836..28e87e00507c 100644
--- a/src/v/pandaproxy/schema_registry/store.h
+++ b/src/v/pandaproxy/schema_registry/store.h
@@ -494,9 +494,19 @@ class store {
     }
 
     ///\brief Clear the compatibility level for a subject.
-    result<bool> clear_compatibility(const subject& sub) {
+    result<bool> clear_compatibility(seq_marker marker, const subject& sub) {
         auto sub_it = BOOST_OUTCOME_TRYX(
           get_subject_iter(sub, include_deleted::yes));
+        auto& markers = sub_it->second.written_at;
+        markers.erase(
+          std::remove_if(
+            markers.begin(),
+            markers.end(),
+            [marker](auto sm) {
+                return sm.key_type == marker.key_type && sm.seq && marker.seq
+                       && *sm.seq == *marker.seq;
+            }),
+          markers.end());
         return std::exchange(sub_it->second.compatibility, std::nullopt)
                != std::nullopt;
     }
diff --git a/src/v/pandaproxy/schema_registry/test/store.cc b/src/v/pandaproxy/schema_registry/test/store.cc
index 37dedae53745..483c0413a8b4 100644
--- a/src/v/pandaproxy/schema_registry/test/store.cc
+++ b/src/v/pandaproxy/schema_registry/test/store.cc
@@ -471,7 +471,8 @@ BOOST_AUTO_TEST_CASE(test_store_subject_compat) {
     BOOST_REQUIRE(s.get_compatibility().value() == global_expected);
 
     // Clearing compatibility should fallback to global
-    BOOST_REQUIRE(s.clear_compatibility(subject0).value() == true);
+    BOOST_REQUIRE(
+      s.clear_compatibility(dummy_marker, subject0).value() == true);
     BOOST_REQUIRE(
       s.get_compatibility(subject0, fallback).value() == global_expected);
 }
@@ -584,7 +585,7 @@ BOOST_AUTO_TEST_CASE(test_store_delete_subject) {
       d_res.error().code(), pps::error_code::subject_soft_deleted);
 
     // Clearing the compatibility of a soft-deleted subject is allowed
-    BOOST_REQUIRE(s.clear_compatibility(subject0).has_value());
+    BOOST_REQUIRE(s.clear_compatibility(dummy_marker, subject0).has_value());
 
     v_res = s.get_versions(subject0, pps::include_deleted::yes);
     BOOST_REQUIRE(v_res.has_value());
@@ -622,7 +623,7 @@ BOOST_AUTO_TEST_CASE(test_store_delete_subject) {
 
     // Clearing the compatibility of a hard-deleted subject should fail
     BOOST_REQUIRE(
-      s.clear_compatibility(subject0).error().code()
+      s.clear_compatibility(dummy_marker, subject0).error().code()
       == pps::error_code::subject_not_found);
 }