diff --git a/main/src/com/google/refine/browsing/Engine.java b/main/src/com/google/refine/browsing/Engine.java
index f0ef66770..4fa193fe1 100644
--- a/main/src/com/google/refine/browsing/Engine.java
+++ b/main/src/com/google/refine/browsing/Engine.java
@@ -44,6 +44,7 @@ import org.json.JSONObject;
 import org.json.JSONWriter;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonValue;
 
 import com.google.refine.Jsonizable;
 import com.google.refine.browsing.facets.Facet;
@@ -72,6 +73,7 @@ public class Engine implements Jsonizable {
 
     protected Project _project;
     protected List<Facet> _facets = new LinkedList<Facet>();
+    @JsonValue
     protected EngineConfig _config = new EngineConfig(Collections.emptyList(), Mode.RowBased);
 
     static public String modeToString(Mode mode) {
diff --git a/main/src/com/google/refine/preference/PreferenceStore.java b/main/src/com/google/refine/preference/PreferenceStore.java
index e44656c6d..7358ad9d1 100644
--- a/main/src/com/google/refine/preference/PreferenceStore.java
+++ b/main/src/com/google/refine/preference/PreferenceStore.java
@@ -33,6 +33,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 package com.google.refine.preference;
 
+import java.io.IOException;
 import java.lang.reflect.Method;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -40,10 +41,18 @@ import java.util.Map;
 import java.util.Properties;
 import java.util.Set;
 
+import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
 import org.json.JSONWriter;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
 import com.google.refine.Jsonizable;
 import com.google.refine.RefineServlet;
 
@@ -54,21 +63,40 @@ public class PreferenceStore implements Jsonizable {
     public static final String USER_NAME = "username";
     
     private boolean dirty = false;
-    protected Map<String, Object> _prefs = new HashMap<String, Object>();
+    protected Map<String, Object> _prefs = new HashMap<>();
+    
+    // Temporary wrapper while serialization has not been migrated yet.
+    @JsonProperty("entries")
+    protected Map<String, Object> _prefsJackson = new HashMap<>();
     
     public void put(String key, Object value) {
         if (value == null) {
             _prefs.remove(key);
+            _prefsJackson.remove(key);
         } else {
             _prefs.put(key, value);
+            _prefsJackson.put(key, wrapJSONArray(value));
         }
         dirty = true;
     }
     
+    private Object wrapJSONArray(Object value) {
+        ObjectMapper mapper = new ObjectMapper();
+        if(value != null && value instanceof JSONArray) {
+            try {
+                return mapper.readValue(value.toString(), JsonNode.class);
+            } catch (IOException e) {
+                return null;
+            }
+        }
+        return value;
+    }
+
     public Object get(String key) {
         return _prefs.get(key);
     }
     
+    @JsonIgnore
     public Set<String> getKeys() {
         return _prefs.keySet();
     }
@@ -98,10 +126,24 @@ public class PreferenceStore implements Jsonizable {
     /**
      * @return true if the preference store has unsaved changes
      */
+    @JsonIgnore
     public boolean isDirty() {
         return dirty;
     }
     
+    /**
+     * Mark the object as clean every time it is serialized.
+     * This behaviour is not very clean - it is inherited from
+     * the previous deserialization code.
+     * @return
+     */
+    @JsonProperty("makeClean")
+    @JsonInclude(Include.NON_NULL)
+    public Integer markAsClean() {
+        dirty = false;
+        return null;
+    }
+    
     @SuppressWarnings("unchecked")
     public void load(JSONObject obj) throws JSONException {
         if (obj.has("entries") && !obj.isNull("entries")) {
@@ -111,8 +153,9 @@ public class PreferenceStore implements Jsonizable {
             while (i.hasNext()) {
                 String key = i.next();
                 if (!entries.isNull(key)) {
-                    Object o = entries.get(key);
-                    _prefs.put(key, loadObject(o));
+                    Object o = entries.get(key), loaded = loadObject(o);
+                    _prefs.put(key, loaded);
+                    _prefsJackson.put(key, wrapJSONArray(loaded));
                 }
             }
             dirty = false; // internal puts don't count
diff --git a/main/src/com/google/refine/preference/TopList.java b/main/src/com/google/refine/preference/TopList.java
index dfc96f9c4..846d579bd 100644
--- a/main/src/com/google/refine/preference/TopList.java
+++ b/main/src/com/google/refine/preference/TopList.java
@@ -44,10 +44,14 @@ import org.json.JSONException;
 import org.json.JSONObject;
 import org.json.JSONWriter;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
 import com.google.refine.Jsonizable;
 
 public class TopList implements Jsonizable, Iterable<String> {
     
+    @JsonProperty("top")
     final protected int          _top;
     final protected List<String> _list = new ArrayList<String>();
 
@@ -56,6 +60,7 @@ public class TopList implements Jsonizable, Iterable<String> {
     }
     
     @SuppressWarnings("unchecked")
+    @JsonProperty("list")
     public List<String> getList() {
         return UnmodifiableList.decorate(_list);
     }
@@ -72,11 +77,16 @@ public class TopList implements Jsonizable, Iterable<String> {
     {
         _list.remove(element);
     }
+    
+    @JsonProperty("class")
+    public String getClassName() {
+        return this.getClass().getName();
+    }
 
     @Override
     public void write(JSONWriter writer, Properties options) throws JSONException {
         writer.object();
-        writer.key("class"); writer.value(this.getClass().getName());
+        writer.key("class"); writer.value(getClassName());
         
         writer.key("top"); writer.value(_top);
         writer.key("list");
@@ -107,7 +117,8 @@ public class TopList implements Jsonizable, Iterable<String> {
         }
     }
     
-    @Override  
+    @Override
+    @JsonIgnore
     public Iterator<String> iterator() {  
         return _list.iterator();  
     } 
diff --git a/main/tests/server/src/com/google/refine/tests/preference/PreferenceStoreTests.java b/main/tests/server/src/com/google/refine/tests/preference/PreferenceStoreTests.java
index 42911dfc5..86778c971 100644
--- a/main/tests/server/src/com/google/refine/tests/preference/PreferenceStoreTests.java
+++ b/main/tests/server/src/com/google/refine/tests/preference/PreferenceStoreTests.java
@@ -1,5 +1,8 @@
 package com.google.refine.tests.preference;
 
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
 import org.json.JSONObject;
 import org.testng.annotations.Test;
 
@@ -17,8 +20,22 @@ public class PreferenceStoreTests {
                 + "   \"scripting.starred-expressions\":{\"class\":\"com.google.refine.preference.TopList\",\"top\":2147483647,\"list\":[]},"
                 + "   \"scripting.expressions\":{\"class\":\"com.google.refine.preference.TopList\",\"top\":100,\"list\":[]}"
                 + "}}";
+        String jsonAfter = "{"
+                + "\"entries\":{"
+                + "   \"reconciliation.standardServices\":["
+                + "           {\"propose_properties\":{\"service_url\":\"https://tools.wmflabs.org/openrefine-wikidata\",\"service_path\":\"/en/propose_properties\"},\"preview\":{\"width\":320,\"url\":\"https://tools.wmflabs.org/openrefine-wikidata/en/preview?id={{id}}\",\"height\":90},\"view\":{\"url\":\"https://www.wikidata.org/wiki/{{id}}\"},\"ui\":{\"handler\":\"ReconStandardServicePanel\"},\"identifierSpace\":\"http://www.wikidata.org/entity/\",\"name\":\"Wikidata Reconciliation for OpenRefine (en)\",\"suggest\":{\"property\":{\"flyout_service_path\":\"/en/flyout/property?id=${id}\",\"service_url\":\"https://tools.wmflabs.org/openrefine-wikidata\",\"service_path\":\"/en/suggest/property\"},\"type\":{\"flyout_service_path\":\"/en/flyout/type?id=${id}\",\"service_url\":\"https://tools.wmflabs.org/openrefine-wikidata\",\"service_path\":\"/en/suggest/type\"},\"entity\":{\"flyout_service_path\":\"/en/flyout/entity?id=${id}\",\"service_url\":\"https://tools.wmflabs.org/openrefine-wikidata\",\"service_path\":\"/en/suggest/entity\"}},\"defaultTypes\":[{\"name\":\"entity\",\"id\":\"Q35120\"}],\"url\":\"https://tools.wmflabs.org/openrefine-wikidata/en/api\",\"schemaSpace\":\"http://www.wikidata.org/prop/direct/\"}"
+                + "        ],"
+                + "   \"scripting.starred-expressions\":{\"class\":\"com.google.refine.preference.TopList\",\"top\":2147483647,\"list\":[]},"
+                + "   \"scripting.expressions\":{\"class\":\"com.google.refine.preference.TopList\",\"top\":100,\"list\":[]},"
+                + "   \"mypreference\":\"myvalue\""
+                + "}}";
         PreferenceStore prefStore = new PreferenceStore();
         prefStore.load(new JSONObject(json));
-        TestUtils.isSerializedTo(prefStore, json);
+        assertFalse(prefStore.isDirty());
+        prefStore.put("mypreference", "myvalue");
+        assertTrue(prefStore.isDirty());
+        TestUtils.isSerializedTo(prefStore, jsonAfter);
+        assertFalse(prefStore.isDirty());
     }
+    
 }