diff --git a/software/core/oqm-core-api/src/main/java/tech/ebp/oqm/core/api/service/mongo/MongoService.java b/software/core/oqm-core-api/src/main/java/tech/ebp/oqm/core/api/service/mongo/MongoService.java
index 03187b0e2..823fe1a36 100644
--- a/software/core/oqm-core-api/src/main/java/tech/ebp/oqm/core/api/service/mongo/MongoService.java
+++ b/software/core/oqm-core-api/src/main/java/tech/ebp/oqm/core/api/service/mongo/MongoService.java
@@ -1,6 +1,7 @@
 package tech.ebp.oqm.core.api.service.mongo;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.mongodb.MongoCommandException;
 import com.mongodb.ReadConcern;
 import com.mongodb.ReadPreference;
 import com.mongodb.TransactionOptions;
@@ -8,6 +9,7 @@
 import com.mongodb.client.ClientSession;
 import com.mongodb.client.MongoClient;
 import com.mongodb.client.MongoCollection;
+import com.mongodb.client.MongoIterable;
 import com.mongodb.client.model.IndexOptions;
 import jakarta.inject.Inject;
 import jakarta.validation.Validation;
@@ -16,13 +18,19 @@
 import lombok.AccessLevel;
 import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
+import org.bson.BsonDocument;
+import org.bson.Document;
 import org.bson.conversions.Bson;
 import org.eclipse.microprofile.config.inject.ConfigProperty;
 import tech.ebp.oqm.core.api.model.collectionStats.CollectionStats;
 import tech.ebp.oqm.core.api.model.object.MainObject;
 import tech.ebp.oqm.core.api.model.rest.search.SearchObject;
 
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * This is the main mongo class. It specifies top level, commonly shared utilities.
@@ -32,92 +40,161 @@
  */
 @Slf4j
 public abstract class MongoService<T extends MainObject, S extends SearchObject<T>, V extends CollectionStats> {
-	
-	//TODO:: move to constructor/inject? Remove?
-	protected static final Validator VALIDATOR;
-
-	static {
-		try (ValidatorFactory validatorFactory = Validation.buildDefaultValidatorFactory()) {
-			VALIDATOR = validatorFactory.getValidator();
-		}
-	}
-
-	/**
-	 * Gets the default transaction options to use for client sessions.
-	 * @return The default transaction options.
-	 */
-	public static TransactionOptions getDefaultTransactionOptions() {
-		return TransactionOptions.builder()
-			.readPreference(ReadPreference.primary())
-			.readConcern(ReadConcern.LOCAL)
-			.writeConcern(WriteConcern.MAJORITY)
-			.build();
-	}
-
-	public ClientSession getNewClientSession(boolean startTransaction) {
-		ClientSession clientSession = this.getMongoClient().startSession();
-
-		if(startTransaction){
-			clientSession.startTransaction();
-		}
-
-		return clientSession;
-	}
-
-	public ClientSession getNewClientSession() {
-		return this.getNewClientSession(false);
-	}
-
-	/**
-	 * The default collection name to use when getting the collection.
-	 * @param clazz The class to get the collection of
-	 * @return The collection name to use when getting the collection.
-	 */
-	public static String getCollectionNameFromClass(Class<?> clazz) {
-		return clazz.getSimpleName();
-	}
-	
-	/**
-	 * The class this collection is in charge of. Used for logging, and other fun.
-	 */
-	@Getter
-	protected final Class<T> clazz;
-	
-	/**
-	 * The MongoDb client.
-	 */
-	@Inject
-	@Getter(AccessLevel.PROTECTED)
-	MongoClient mongoClient;
-
-	/**
-	 * Mapper to help deal with json updates.
-	 */
-	@Inject
-	@Getter(AccessLevel.PROTECTED)
-	ObjectMapper objectMapper;
-
-	/**
-	 * The name of the database to access
-	 */
-	@Getter
-	@ConfigProperty(name = "quarkus.mongodb.database")
-	String databasePrefix;
-
-	public MongoService(Class<T> clazz) {
-		this.clazz = clazz;
-	}
-	
-	public abstract int getCurrentSchemaVersion();
-
-	public abstract List<Bson> getDbIndexes();
-
-	public abstract void initDb();
-
-	protected static void setupIndexes(MongoCollection<?> collection, List<Bson> indexes) {
-		IndexOptions options = new IndexOptions().background(true);
-		for (Bson index : indexes) {
-			collection.createIndex(index, options);
-		}
-	}
+
+    // TODO:: move to constructor/inject? Remove?
+    protected static final Validator VALIDATOR;
+
+    static {
+        try (ValidatorFactory validatorFactory = Validation.buildDefaultValidatorFactory()) {
+            VALIDATOR = validatorFactory.getValidator();
+        }
+    }
+
+    /**
+     * Gets the default transaction options to use for client sessions.
+     *
+     * @return The default transaction options.
+     */
+    public static TransactionOptions getDefaultTransactionOptions() {
+        return TransactionOptions.builder().readPreference(ReadPreference.primary()).readConcern(ReadConcern.LOCAL).writeConcern(WriteConcern.MAJORITY).build();
+    }
+
+    public ClientSession getNewClientSession(boolean startTransaction) {
+        ClientSession clientSession = this.getMongoClient().startSession();
+
+        if (startTransaction) {
+            clientSession.startTransaction();
+        }
+
+        return clientSession;
+    }
+
+    public ClientSession getNewClientSession() {
+        return this.getNewClientSession(false);
+    }
+
+    /**
+     * The default collection name to use when getting the collection.
+     *
+     * @param clazz The class to get the collection of
+     * @return The collection name to use when getting the collection.
+     */
+    public static String getCollectionNameFromClass(Class<?> clazz) {
+        return clazz.getSimpleName();
+    }
+
+    /**
+     * The class this collection is in charge of. Used for logging, and other fun.
+     */
+    @Getter
+    protected final Class<T> clazz;
+
+    /**
+     * The MongoDb client.
+     */
+    @Inject
+    @Getter(AccessLevel.PROTECTED)
+    MongoClient mongoClient;
+
+    /**
+     * Mapper to help deal with json updates.
+     */
+    @Inject
+    @Getter(AccessLevel.PROTECTED)
+    ObjectMapper objectMapper;
+
+    /**
+     * The name of the database to access
+     */
+    @Getter
+    @ConfigProperty(name = "quarkus.mongodb.database")
+    String databasePrefix;
+
+    public MongoService(Class<T> clazz) {
+        this.clazz = clazz;
+    }
+
+    public abstract int getCurrentSchemaVersion();
+
+    public abstract List<Bson> getDbIndexes();
+
+    public abstract void initDb();
+
+    /**
+     * Sets up indexes for the given MongoDB collection.
+     * All expected indexes are (re)created on each call, and if an index already exists, it is dropped
+     * and recreated to ensure its options are always up to date.
+     * Indexes no longer present in the expected list are dropped.
+     * The default {@code _id_} index is never dropped.
+     *
+     * @param collection the MongoDB collection to manage indexes on
+     * @param indexes    the list of indexes that should exist on the collection
+     */
+    protected static void setupIndexes(MongoCollection<?> collection, List<Bson> indexes) {
+        log.info("setting up indexes for collection {}", collection.getNamespace());
+        IndexOptions options = new IndexOptions().background(true);
+        Map<BsonDocument, String> existingIndexes = getExistingIndexes(collection);
+        Set<BsonDocument> expectedKeys = new HashSet<>();
+
+        for (Bson index : indexes) {
+            BsonDocument expectedKey = index.toBsonDocument(BsonDocument.class, collection.getCodecRegistry());
+            expectedKeys.add(expectedKey);
+            log.info("ensuring index with key {}", expectedKey);
+            if (existingIndexes.containsKey(expectedKey)) {
+                try {
+                    collection.createIndex(index, options);
+                } catch (MongoCommandException e) {
+                    log.warn("failed to create index with key {}, dropping and recreating index", expectedKey, e);
+                    collection.dropIndex(existingIndexes.get(expectedKey));
+                    collection.createIndex(index, options);
+                }
+            } else {
+                collection.createIndex(index, options);
+            }
+        }
+
+        for (Map.Entry<BsonDocument, String> existing : existingIndexes.entrySet()) {
+            if (!expectedKeys.contains(existing.getKey())) {
+                log.info("dropping index with key {}", existing.getKey());
+                collection.dropIndex(existing.getValue());
+            }
+        }
+    }
+
+    /**
+     * Returns a map of existing indexes on the given collection ignoring the default <b>_id_</b> index.
+     * Input Index:
+     * <pre>
+     * {@code
+     * Indexes.ascending("name")
+     * }
+     * </pre>
+     *
+     * Would produce:
+     * <pre>
+     * {@code
+     *   Key: {"name": 1}
+     *   Value: "name_1"
+     * }
+     * </pre>
+     *
+     * @param collection the MongoDB collection to read indexes from
+     * @return map of index key document to index name
+     */
+    private static Map<BsonDocument, String> getExistingIndexes(MongoCollection<?> collection) {
+        MongoIterable<Document> existingDocument = collection.listIndexes();
+        Map<BsonDocument, String> existingIndexes = new HashMap<>();
+        for (Document doc : existingDocument) {
+            Document keyDoc = doc.get("key", Document.class);
+            if (keyDoc == null) {
+                continue;
+            }
+            BsonDocument key = keyDoc.toBsonDocument(BsonDocument.class, collection.getCodecRegistry());
+            String name = doc.getString("name");
+            if (name != null && !name.equals("_id_")) {
+                existingIndexes.put(key, name);
+            }
+        }
+        return existingIndexes;
+    }
 }