diff --git a/infrastructures/kubernetes/src/main/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMerger.java b/infrastructures/kubernetes/src/main/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMerger.java
index 20faca5d7e..85d7370155 100644
--- a/infrastructures/kubernetes/src/main/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMerger.java
+++ b/infrastructures/kubernetes/src/main/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMerger.java
@@ -23,6 +23,7 @@ import io.fabric8.kubernetes.api.model.ObjectMetaBuilder;
 import io.fabric8.kubernetes.api.model.PodSecurityContext;
 import io.fabric8.kubernetes.api.model.PodSpec;
 import io.fabric8.kubernetes.api.model.PodTemplateSpec;
+import io.fabric8.kubernetes.api.model.Toleration;
 import io.fabric8.kubernetes.api.model.Volume;
 import io.fabric8.kubernetes.api.model.apps.Deployment;
 import io.fabric8.kubernetes.api.model.apps.DeploymentBuilder;
@@ -154,8 +155,13 @@ public class PodMerger {
 
       // if there are entries with such keys then values will be overridden
       baseSpec.getAdditionalProperties().putAll(podData.getSpec().getAdditionalProperties());
+
       // add tolerations to baseSpec if any
-      baseSpec.getTolerations().addAll(podData.getSpec().getTolerations());
+      for (Toleration toleration : podData.getSpec().getTolerations()) {
+        if (!baseSpec.getTolerations().contains(toleration)) {
+          baseSpec.getTolerations().add(toleration);
+        }
+      }
     }
 
     Map<String, String> matchLabels = new HashMap<>();
diff --git a/infrastructures/kubernetes/src/test/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMergerTest.java b/infrastructures/kubernetes/src/test/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMergerTest.java
index 16befa69b9..a0220e39cb 100644
--- a/infrastructures/kubernetes/src/test/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMergerTest.java
+++ b/infrastructures/kubernetes/src/test/java/org/eclipse/che/workspace/infrastructure/kubernetes/environment/PodMergerTest.java
@@ -33,6 +33,7 @@ import io.fabric8.kubernetes.api.model.VolumeBuilder;
 import io.fabric8.kubernetes.api.model.apps.Deployment;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -131,7 +132,9 @@ public class PodMergerTest {
             .withVolumes(new VolumeBuilder().withName("v2").build())
             .withNodeSelector(Map.of("foo2", "bar2"))
             .withImagePullSecrets(new LocalObjectReferenceBuilder().withName("secret2").build())
-            .withTolerations(new Toleration("Effect", "key", "operator", 0L, "value2"))
+            .withTolerations(
+                new Toleration("Effect", "key", "operator", 0L, "value1"),
+                new Toleration("Effect", "key", "operator", 0L, "value2"))
             .build();
     podSpec2.setAdditionalProperty("add2", 2L);
     PodData podData2 = new PodData(podSpec2, new ObjectMetaBuilder().build());
@@ -452,5 +455,6 @@ public class PodMergerTest {
             .entrySet()
             .containsAll(toCheck.getAdditionalProperties().entrySet()));
     assertTrue(source.getTolerations().containsAll(toCheck.getTolerations()));
+    assertEquals(toCheck.getTolerations().size(), new HashSet<>(toCheck.getTolerations()).size());
   }
 }