diff --git a/src/libslic3r/PrintConfig.hpp b/src/libslic3r/PrintConfig.hpp
index b6364c32c2..f51c1c6411 100644
--- a/src/libslic3r/PrintConfig.hpp
+++ b/src/libslic3r/PrintConfig.hpp
@@ -2397,6 +2397,55 @@ static void set_flush_volumes_matrix(std::vector<T> &out_matrix, const std::vect
     }
 }
 
+template<class T>
+static bool has_zero_flush_volume_for_used_filaments(const std::vector<T> &fv_matrix,
+                                                      const std::vector<T> &flush_multipliers,
+                                                      const std::vector<int> &used_filaments)
+{
+    if (used_filaments.size() < 2 || flush_multipliers.empty())
+        return false;
+
+    if (fv_matrix.size() % flush_multipliers.size() != 0)
+        return false;
+
+    const size_t matrix_len = fv_matrix.size() / flush_multipliers.size();
+    const size_t row_len    = size_t(std::sqrt(double(matrix_len)));
+    if (row_len < 2 || row_len * row_len != matrix_len)
+        return false;
+
+    std::vector<int> filtered_filaments;
+    filtered_filaments.reserve(used_filaments.size());
+    for (int filament_id : used_filaments) {
+        if (filament_id <= 0 || filament_id > int(row_len))
+            continue;
+        if (std::find(filtered_filaments.begin(), filtered_filaments.end(), filament_id) == filtered_filaments.end())
+            filtered_filaments.push_back(filament_id);
+    }
+    if (filtered_filaments.size() < 2)
+        return false;
+
+    for (T multiplier : flush_multipliers) {
+        if (multiplier == 0)
+            return true;
+    }
+
+    for (size_t nozzle_idx = 0; nozzle_idx < flush_multipliers.size(); nozzle_idx++) {
+        const size_t block_offset = nozzle_idx * matrix_len;
+        for (int from_id : filtered_filaments) {
+            for (int to_id : filtered_filaments) {
+                if (from_id == to_id)
+                    continue;
+
+                const size_t matrix_idx = block_offset + size_t(from_id - 1) * row_len + size_t(to_id - 1);
+                if (matrix_idx < fv_matrix.size() && fv_matrix[matrix_idx] == 0)
+                    return true;
+            }
+        }
+    }
+
+    return false;
+}
+
 size_t get_extruder_index(const GCodeConfig& config, unsigned int filament_id);
 
 } // namespace Slic3r
diff --git a/src/slic3r/GUI/GLCanvas3D.cpp b/src/slic3r/GUI/GLCanvas3D.cpp
index 303f9a2b76..d0eb79881b 100644
--- a/src/slic3r/GUI/GLCanvas3D.cpp
+++ b/src/slic3r/GUI/GLCanvas3D.cpp
@@ -10738,24 +10738,14 @@ bool GLCanvas3D::is_flushing_matrix_error() {
     if (!Sidebar::should_show_SEMM_buttons())
         return false;
 
+    std::vector<int> plate_extruders = wxGetApp().plater()->get_partplate_list().get_curr_plate()->get_extruders(true);
+    if (plate_extruders.size() < 2)
+        return false;
+
     const auto                &project_config = wxGetApp().preset_bundle->project_config;
     const std::vector<double> &config_matrix  = (project_config.option<ConfigOptionFloats>("flush_volumes_matrix"))->values;
     const std::vector<double> &config_multiplier = (project_config.option<ConfigOptionFloats>("flush_multiplier"))->values;
-
-    for (auto multiplier : config_multiplier) {
-        if (multiplier == 0) return true;
-    }
-
-    int  matrix_len = config_matrix.size() / config_multiplier.size();
-    int  row_len    = std::sqrt(matrix_len);
-    for (int i = 0; i < config_matrix.size(); i++)
-    {
-        int relative_id = i % matrix_len;
-        int row_id      = relative_id / row_len;
-        int col_id      = relative_id % row_len;
-        if (row_id != col_id && config_matrix[i] == 0) return true;
-    }
-    return false;
+    return has_zero_flush_volume_for_used_filaments(config_matrix, config_multiplier, plate_extruders);
 }
 
 bool GLCanvas3D::_is_any_volume_outside() const
diff --git a/tests/libslic3r/test_config.cpp b/tests/libslic3r/test_config.cpp
index 5bc825c3b2..12b161322d 100644
--- a/tests/libslic3r/test_config.cpp
+++ b/tests/libslic3r/test_config.cpp
@@ -235,6 +235,56 @@ SCENARIO("Config ini load/save interface", "[Config]") {
     }
 }
 
+TEST_CASE("Flush-volume warning predicate respects used filament transitions", "[Config][Regression]")
+{
+    const std::vector<double> multipliers = {1.0};
+
+    SECTION("Single used filament does not trigger warning with zero transition entries")
+    {
+        const std::vector<double> matrix = {
+            0.0, 0.0,
+            0.0, 0.0
+        };
+        const std::vector<int> used_filaments = {1};
+
+        REQUIRE_FALSE(has_zero_flush_volume_for_used_filaments(matrix, multipliers, used_filaments));
+    }
+
+    SECTION("Two used filaments trigger warning when transition flush entry is zero")
+    {
+        const std::vector<double> matrix = {
+            0.0, 0.0,
+            0.0, 0.0
+        };
+        const std::vector<int> used_filaments = {1, 2};
+
+        REQUIRE(has_zero_flush_volume_for_used_filaments(matrix, multipliers, used_filaments));
+    }
+
+    SECTION("Two used filaments do not trigger warning when transitions are non-zero")
+    {
+        const std::vector<double> matrix = {
+            0.0, 280.0,
+            280.0, 0.0
+        };
+        const std::vector<int> used_filaments = {1, 2};
+
+        REQUIRE_FALSE(has_zero_flush_volume_for_used_filaments(matrix, multipliers, used_filaments));
+    }
+
+    SECTION("Zero multiplier still triggers warning when multiple filaments are used")
+    {
+        const std::vector<double> matrix = {
+            0.0, 280.0,
+            280.0, 0.0
+        };
+        const std::vector<double> zero_multiplier = {0.0};
+        const std::vector<int> used_filaments = {1, 2};
+
+        REQUIRE(has_zero_flush_volume_for_used_filaments(matrix, zero_multiplier, used_filaments));
+    }
+}
+
 // TODO: https://github.com/SoftFever/OrcaSlicer/issues/11269 - Is this test still relevant? Delete if not.
 // It was failing so at least "nozzle_type" and "extruder_printable_area" could not be serialized
 // and an exception was thrown, but "nozzle_type" has been around for at least 3 months now.