diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/datasource/NCBIAssemblyDataSource.java b/src/main/java/uk/ac/ebi/eva/contigalias/datasource/NCBIAssemblyDataSource.java
index f798dd66..b6438d75 100644
--- a/src/main/java/uk/ac/ebi/eva/contigalias/datasource/NCBIAssemblyDataSource.java
+++ b/src/main/java/uk/ac/ebi/eva/contigalias/datasource/NCBIAssemblyDataSource.java
@@ -34,7 +34,6 @@
 import uk.ac.ebi.eva.contigalias.repo.AssemblyRepository;
 import uk.ac.ebi.eva.contigalias.repo.ChromosomeRepository;
 
-import javax.transaction.Transactional;
 import java.io.BufferedReader;
 import java.io.FileInputStream;
 import java.io.FileReader;
@@ -165,7 +164,6 @@ public Optional<Path> downloadAssemblyReport(String accession, NCBIBrowser ncbiB
         }
     }
 
-    @Transactional
     public void parseFileAndInsertAssembly(String accession, ENAAssemblyDataSource enaDataSource,
                                            AssemblyRepository assemblyRepository, ChromosomeRepository chromosomeRepository) throws IOException {
         Optional<Path> downloadNCBIFilePathOpt = downloadAssemblyReport(accession);
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/exception/AssemblyIngestionException.java b/src/main/java/uk/ac/ebi/eva/contigalias/exception/AssemblyIngestionException.java
new file mode 100644
index 00000000..c60b42ac
--- /dev/null
+++ b/src/main/java/uk/ac/ebi/eva/contigalias/exception/AssemblyIngestionException.java
@@ -0,0 +1,8 @@
+package uk.ac.ebi.eva.contigalias.exception;
+
+public class AssemblyIngestionException extends RuntimeException {
+
+    public AssemblyIngestionException(String accession) {
+        super("Error Ingesting assembly with accession " + accession);
+    }
+}
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/exception/ControllerExceptionHandler.java b/src/main/java/uk/ac/ebi/eva/contigalias/exception/ControllerExceptionHandler.java
index 93d5c868..2d6c0d3b 100644
--- a/src/main/java/uk/ac/ebi/eva/contigalias/exception/ControllerExceptionHandler.java
+++ b/src/main/java/uk/ac/ebi/eva/contigalias/exception/ControllerExceptionHandler.java
@@ -30,4 +30,9 @@ public ResponseEntity<String> handleExceptions(DownloadFailedException exception
         return new ResponseEntity<>(exception.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
     }
 
+    @ExceptionHandler(AssemblyIngestionException.class)
+    public ResponseEntity<String> handleExceptions(AssemblyIngestionException exception, WebRequest webRequest){
+        return new ResponseEntity<>(exception.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
+    }
+
 }
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/repo/AssemblyRepository.java b/src/main/java/uk/ac/ebi/eva/contigalias/repo/AssemblyRepository.java
index 9ffe65d8..62881539 100644
--- a/src/main/java/uk/ac/ebi/eva/contigalias/repo/AssemblyRepository.java
+++ b/src/main/java/uk/ac/ebi/eva/contigalias/repo/AssemblyRepository.java
@@ -20,6 +20,9 @@
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 import org.springframework.stereotype.Repository;
 
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
@@ -46,8 +49,17 @@ default Optional<AssemblyEntity> findAssemblyEntityByAccession(String accession)
     Page<AssemblyEntity> findAssemblyEntitiesByTaxid(long taxid, Pageable pageable);
 
     @Transactional
-    void deleteAssemblyEntityByInsdcAccession(String insdcAccession);
+    @Modifying
+    @Query("DELETE FROM AssemblyEntity a WHERE a.insdcAccession=:asmInsdcAccession")
+    void deleteAssemblyEntityByInsdcAccession(@Param("asmInsdcAccession") String asmInsdcAccession);
 
     @Transactional
-    void deleteAssemblyEntityByRefseq(String refseq);
+    @Modifying
+    @Query("DELETE FROM AssemblyEntity a WHERE a.refseq=:asmRefSeq")
+    void deleteAssemblyEntityByRefseq(@Param("asmRefSeq") String asmRefSeq);
+
+    @Transactional
+    @Modifying
+    @Query("DELETE FROM AssemblyEntity a WHERE a.insdcAccession=:asmAccession OR a.refseq=:asmAccession")
+    void deleteAssemblyEntityByInsdcAccessionOrRefseq(@Param("asmAccession") String asmAccession);
 }
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/repo/ChromosomeRepository.java b/src/main/java/uk/ac/ebi/eva/contigalias/repo/ChromosomeRepository.java
index 2a1ae338..bf3d2784 100644
--- a/src/main/java/uk/ac/ebi/eva/contigalias/repo/ChromosomeRepository.java
+++ b/src/main/java/uk/ac/ebi/eva/contigalias/repo/ChromosomeRepository.java
@@ -27,6 +27,7 @@
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
 
+import javax.transaction.Transactional;
 import java.util.List;
 
 @Repository
@@ -50,6 +51,11 @@ public interface ChromosomeRepository extends JpaRepository<ChromosomeEntity, Lo
     @Query("UPDATE ChromosomeEntity c SET c.md5checksum = :md5Checksum WHERE c.assembly.insdcAccession= :asmInsdcAccession AND c.insdcAccession = :insdcAccession")
     void updateMd5ChecksumByInsdcAccession(@Param("asmInsdcAccession") String asmInsdcAccession, @Param("insdcAccession") String insdcAccession, @Param("md5Checksum") String md5Checksum);
 
+    @Transactional
+    @Modifying
+    @Query("DELETE FROM ChromosomeEntity c WHERE c.assembly.insdcAccession=:asmInsdcAccession")
+    void deleteChromosomeEntitiesByAssembly_InsdcAccession(@Param("asmInsdcAccession") String asmInsdcAccession);
+
     Page<ChromosomeEntity> findChromosomeEntitiesByAssembly_Refseq(String asmRefseq, Pageable request);
 
     Page<ChromosomeEntity> findChromosomeEntitiesByGenbankSequenceNameAndAssembly_Taxid(String genbankName, long asmTaxid, Pageable request);
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/ChecksumSetter.java b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/ChecksumSetter.java
index 564b50ca..f6ff960f 100644
--- a/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/ChecksumSetter.java
+++ b/src/main/java/uk/ac/ebi/eva/contigalias/scheduler/ChecksumSetter.java
@@ -17,7 +17,6 @@
 import java.util.Set;
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.ConcurrentHashMap;
-import java.util.concurrent.ExecutionException;
 
 @Component
 public class ChecksumSetter {
@@ -48,7 +47,7 @@ public void updateMd5CheckSumForAllAssemblies() {
             CompletableFuture<Void> future = updateMd5CheckSumForAssemblyAsync(assembly);
             try {
                 future.get();
-            } catch (InterruptedException | ExecutionException e) {
+            } catch (Exception e) {
                 logger.error("Encountered an error when running MD5Checksum update for assembly: " + assembly);
             } finally {
                 scheduledToRunMD5ChecksumUpdateTasks.remove(assembly);
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java b/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java
index 2365181b..ad373682 100644
--- a/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java
+++ b/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java
@@ -26,6 +26,7 @@
 import uk.ac.ebi.eva.contigalias.datasource.NCBIAssemblyDataSource;
 import uk.ac.ebi.eva.contigalias.entities.AssemblyEntity;
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
+import uk.ac.ebi.eva.contigalias.exception.AssemblyIngestionException;
 import uk.ac.ebi.eva.contigalias.exception.AssemblyNotFoundException;
 import uk.ac.ebi.eva.contigalias.exception.DuplicateAssemblyException;
 import uk.ac.ebi.eva.contigalias.repo.AssemblyRepository;
@@ -105,12 +106,24 @@ public void fetchAndInsertAssembly(String accession) throws IOException {
             throw duplicateAssemblyInsertionException(accession, entity.get());
         }
 
-        // download file and save assembly and chromosome data
-        ncbiDataSource.parseFileAndInsertAssembly(accession, enaDataSource, assemblyRepository, chromosomeRepository);
-        logger.info("Successfully inserted assembly for accession " + accession);
+        try {
+            // download file and save assembly and chromosome data
+            ncbiDataSource.parseFileAndInsertAssembly(accession, enaDataSource, assemblyRepository, chromosomeRepository);
+            logger.info("Successfully inserted assembly for accession " + accession);
+
+            // submit job for retrieving and updating MD5 Checksum for assembly (asynchronously)
+            checksumSetter.updateMd5CheckSumForAssemblyAsync(accession);
+        } catch (Exception e) {
+            // roll back inserted entries in case of any exception or error
+            logger.error("Exception while inserting assembly " + accession + " Rolling back changes");
+            deleteEntriesForAssembly(accession);
+            throw new AssemblyIngestionException(accession);
+        }
+    }
 
-        // submit job for retrieving and updating MD5 Checksum for assembly (asynchronously)
-        checksumSetter.updateMd5CheckSumForAssemblyAsync(accession);
+    public void deleteEntriesForAssembly(String accession) {
+        chromosomeRepository.deleteChromosomeEntitiesByAssembly_InsdcAccession(accession);
+        assemblyRepository.deleteAssemblyEntityByInsdcAccessionOrRefseq(accession);
     }
 
     public void retrieveAndInsertMd5ChecksumForAssembly(String assembly) {