diff --git a/src/api/controller/api/publishFacets.js b/src/api/controller/api/publishFacets.js
index 23bc09840..205cff221 100644
--- a/src/api/controller/api/publishFacets.js
+++ b/src/api/controller/api/publishFacets.js
@@ -19,7 +19,7 @@ export default async (ctx, fields, withProgress = false) => {
     jobLogger.info(ctx.job, 'Publishing facets');
 
     const names = fields.map(({ name }) => name);
-    await ctx.publishedFacet.remove({ field: { $in: names } });
+    await ctx.publishedFacet.deleteOne({ field: { $in: names } });
 
     await facetFields
         .reduce(
diff --git a/src/api/controller/testController.js b/src/api/controller/testController.js
index 316334f48..2653791de 100644
--- a/src/api/controller/testController.js
+++ b/src/api/controller/testController.js
@@ -16,15 +16,15 @@ app.use(mongoRootAdminClient);
 
 app.use(
     route.delete('/fixtures', async (ctx) => {
-        await ctx.db.collection('publishedDataset').remove({});
-        await ctx.db.collection('publishedCharacteristic').remove({});
-        await ctx.db.collection('field').remove({});
-        await ctx.db.collection('dataset').remove({});
-        await ctx.db.collection('subresource').remove({});
-        await ctx.db.collection('enrichment').remove({});
+        await ctx.db.collection('publishedDataset').drop();
+        await ctx.db.collection('publishedCharacteristic').drop();
+        await ctx.db.collection('field').drop();
+        await ctx.db.collection('dataset').drop();
+        await ctx.db.collection('subresource').drop();
+        await ctx.db.collection('enrichment').drop();
         await ctx.rootAdminDb
             .collection('tenant')
-            .remove({ name: { $ne: DEFAULT_TENANT } });
+            .deleteOne({ name: { $ne: DEFAULT_TENANT } });
         ctx.body = { status: 'ok' };
     }),
 );
diff --git a/src/api/models/configTenant.js b/src/api/models/configTenant.js
index d4a13d4a5..dfc9ce13f 100644
--- a/src/api/models/configTenant.js
+++ b/src/api/models/configTenant.js
@@ -28,7 +28,7 @@ export default async (db) => {
     };
 
     collection.delete = async (id) =>
-        collection.remove({ $or: [{ _id: new ObjectId(id) }, { _id: id }] });
+        collection.deleteOne({ $or: [{ _id: new ObjectId(id) }, { _id: id }] });
 
     collection.update = async (id, data) => {
         const objectId = new ObjectId(id);
diff --git a/src/api/models/dataset.js b/src/api/models/dataset.js
index 37ec407a4..e6ff38ca3 100644
--- a/src/api/models/dataset.js
+++ b/src/api/models/dataset.js
@@ -141,7 +141,7 @@ export default (db) => {
     };
 
     collection.removeAttribute = async (attribute) =>
-        collection.update({}, { $unset: { [attribute]: 1 } }, { multi: true });
+        collection.updateOne({}, { $unset: { [attribute]: 1 } }, { multi: true });
 
     collection.findBy = async (fieldName, value) => {
         if (!(await collection.ensureIsUnique(fieldName))) {
@@ -201,7 +201,7 @@ export default (db) => {
     };
 
     collection.deleteOne = async (id) =>
-        collection.remove({ _id: new ObjectID(id) });
+        collection.deleteOne({ _id: new ObjectID(id) });
 
     return collection;
 };
diff --git a/src/api/models/enrichment.js b/src/api/models/enrichment.js
index 6c3492054..c0d8067aa 100644
--- a/src/api/models/enrichment.js
+++ b/src/api/models/enrichment.js
@@ -17,7 +17,7 @@ export default async (db) => {
     };
 
     collection.delete = async (id) =>
-        collection.remove({ $or: [{ _id: new ObjectId(id) }, { _id: id }] });
+        collection.deleteOne({ $or: [{ _id: new ObjectId(id) }, { _id: id }] });
 
     collection.update = async (id, data) => {
         const objectId = new ObjectId(id);
diff --git a/src/api/models/field.js b/src/api/models/field.js
index 1baa8d796..c73935645 100644
--- a/src/api/models/field.js
+++ b/src/api/models/field.js
@@ -203,10 +203,10 @@ export default async (db) => {
     };
 
     collection.removeById = (id) =>
-        collection.remove({ _id: new ObjectID(id), name: { $ne: 'uri' } });
+        collection.deleteOne({ _id: new ObjectID(id), name: { $ne: 'uri' } });
 
     collection.removeBySubresource = (subresourceId) =>
-        collection.remove({
+        collection.deleteOne({
             $or: [
                 { subresourceId: new ObjectID(subresourceId) },
                 { subresourceId },
@@ -261,7 +261,7 @@ export default async (db) => {
         }
 
         if (isLogged) {
-            await collection.update(
+            await collection.updateOne(
                 {
                     name,
                     contribution: true,
@@ -278,7 +278,7 @@ export default async (db) => {
             return name;
         }
 
-        await collection.update(
+        await collection.updateOne(
             {
                 name,
                 contribution: true,
diff --git a/src/api/models/hiddenResource.js b/src/api/models/hiddenResource.js
index 32452a592..7b973df58 100644
--- a/src/api/models/hiddenResource.js
+++ b/src/api/models/hiddenResource.js
@@ -18,7 +18,7 @@ export default async (db) => {
     collection.deleteByUri = async (uri) => collection.deleteOne({ uri });
 
     collection.delete = async (id) =>
-        collection.remove({ _id: new ObjectID(id) });
+        collection.deleteOne({ _id: new ObjectID(id) });
 
     collection.castIds = castIdsFactory(collection);
 
diff --git a/src/api/models/precomputed.js b/src/api/models/precomputed.js
index 1ed75a075..cd1e3b9bb 100644
--- a/src/api/models/precomputed.js
+++ b/src/api/models/precomputed.js
@@ -35,7 +35,7 @@ export default async (db) => {
             // Collection does not exist, no big deal
             console.warn(`Failed to drop collection 'pc_${id}'`);
         }
-        return collection.remove({
+        return collection.deleteOne({
             $or: [{ _id: new ObjectId(id) }, { _id: id }],
         });
     };
diff --git a/src/api/models/publishedDataset.js b/src/api/models/publishedDataset.js
index 2ea88347b..8871cce74 100644
--- a/src/api/models/publishedDataset.js
+++ b/src/api/models/publishedDataset.js
@@ -52,7 +52,7 @@ export default async (db) => {
     collection.insertBatchIgnoreDuplicate = (documents) =>
         Promise.all(
             chunk(documents, 1000).map((data) =>
-                collection.insert(data, { ordered: false }).catch((e) => {
+                collection.insertOne(data, { ordered: false }).catch((e) => {
                     if (e.code === 11000 /* duplicate error */) {
                         return;
                     }
@@ -228,7 +228,7 @@ export default async (db) => {
         );
 
     collection.hide = async (uri, reason, date = new Date()) => {
-        await collection.update(
+        await collection.updateOne(
             { uri },
             {
                 $set: {
@@ -242,7 +242,7 @@ export default async (db) => {
     };
 
     collection.restore = async (uri) =>
-        collection.update(
+        collection.updateOne(
             { uri },
             { $unset: { removedAt: true, reason: true } },
         );
@@ -262,7 +262,7 @@ export default async (db) => {
             publicationDate,
         };
 
-        return collection.update(
+        return collection.updateOne(
             { uri },
             {
                 $addToSet: {
@@ -312,7 +312,7 @@ export default async (db) => {
             return { result: 'noChange' };
         }
 
-        await collection.update(
+        await collection.updateOne(
             {
                 uri,
                 'contributions.fieldName': name,
diff --git a/src/api/models/subresource.js b/src/api/models/subresource.js
index 7e5921f9c..525451778 100644
--- a/src/api/models/subresource.js
+++ b/src/api/models/subresource.js
@@ -16,7 +16,7 @@ export default async (db) => {
     };
 
     collection.delete = async (id) =>
-        collection.remove({ _id: new ObjectID(id) });
+        collection.deleteOne({ _id: new ObjectID(id) });
 
     collection.update = async (id, data) => {
         const objectId = new ObjectID(id);
diff --git a/src/api/models/tenant.js b/src/api/models/tenant.js
index ae0f9523c..b5f990c16 100644
--- a/src/api/models/tenant.js
+++ b/src/api/models/tenant.js
@@ -20,7 +20,7 @@ export default async (db) => {
     };
 
     collection.delete = async (id) =>
-        collection.remove({ $or: [{ _id: new ObjectID(id) }, { _id: id }] });
+        collection.deleteOne({ $or: [{ _id: new ObjectID(id) }, { _id: id }] });
 
     collection.update = async (id, data) => {
         const objectId = new ObjectID(id);
diff --git a/src/api/models/utils.js b/src/api/models/utils.js
index 2bfc1947c..52b3672ec 100644
--- a/src/api/models/utils.js
+++ b/src/api/models/utils.js
@@ -7,8 +7,8 @@ export const castIdsFactory = (collection) => async () => {
         (acc, item) =>
             acc.then(async () => {
                 await acc;
-                await collection.remove({ _id: item._id });
-                await collection.insert({
+                await collection.removeOne({ _id: item._id });
+                await collection.insertOne({
                     ...item,
                     _id: new ObjectID(item._id),
                 });
diff --git a/src/api/services/enrichment/enrichment.js b/src/api/services/enrichment/enrichment.js
index 083304aaf..bb70cfc5a 100644
--- a/src/api/services/enrichment/enrichment.js
+++ b/src/api/services/enrichment/enrichment.js
@@ -423,7 +423,7 @@ export const restoreEnrichments = async (ctx) => {
                 ctx,
                 enrichment,
             );
-            await ctx.enrichment.update(enrichment._id, enrichmentWithRule);
+            await ctx.enrichment.updateOne(enrichment._id, enrichmentWithRule);
         }
     }
 };
diff --git a/src/api/services/saveParsedStream.js b/src/api/services/saveParsedStream.js
index 0ae0132f4..6ff99b992 100644
--- a/src/api/services/saveParsedStream.js
+++ b/src/api/services/saveParsedStream.js
@@ -41,8 +41,8 @@ export const saveParsedStream = async (ctx, parsedStream) => {
 
         return ctx.dataset.count();
     } catch (error) {
-        await ctx.dataset.remove({ lodex_published: { $exists: false } });
-        await ctx.publishedDataset.remove({
+        await ctx.dataset.deleteOne({ lodex_published: { $exists: false } });
+        await ctx.publishedDataset.deleteOne({
             lodex_published: { $exists: false },
         });
 
diff --git a/src/api/services/updateFacetValue.js b/src/api/services/updateFacetValue.js
index 0675c91ca..cc4eef1fc 100644
--- a/src/api/services/updateFacetValue.js
+++ b/src/api/services/updateFacetValue.js
@@ -13,7 +13,7 @@ const removeOldValue = (publishedFacet, field) => async (oldValue) => {
 };
 
 const addNewValue = (publishedFacet, field) => async (newValue) => {
-    await publishedFacet.update(
+    await publishedFacet.updateOne(
         { field, value: newValue },
         { $inc: { count: 1 } },
         { upsert: true },
diff --git a/src/common/tests/fixtures.js b/src/common/tests/fixtures.js
index 3f253b159..b7185a502 100644
--- a/src/common/tests/fixtures.js
+++ b/src/common/tests/fixtures.js
@@ -57,11 +57,11 @@ export async function clear() {
     }
 
     await Promise.all([
-        db.dataset.remove({}),
-        db.field.remove({}),
-        db.publishedCharacteristic.remove({}),
-        db.publishedDataset.remove({}),
-        db.publishedFacet.remove({}),
+        db.dataset.drop(),
+        db.field.drop(),
+        db.publishedCharacteristic.drop(),
+        db.publishedDataset.drop(),
+        db.publishedFacet.drop(),
     ]);
 
     return db;