diff --git a/packages/backend-core/src/sql/sql.ts b/packages/backend-core/src/sql/sql.ts
index 9b6819d433..e6738d4b36 100644
--- a/packages/backend-core/src/sql/sql.ts
+++ b/packages/backend-core/src/sql/sql.ts
@@ -337,6 +337,11 @@ class InternalBuilder {
     return filters
   }
 
+  addJoinFieldCheck(query: Knex.QueryBuilder, relationship: RelationshipsJson) {
+    const document = relationship.from?.split(".")[0] || ""
+    return query.andWhere(`${document}.fieldName`, "=", relationship.column)
+  }
+
   addRelationshipForFilter(
     query: Knex.QueryBuilder,
     filterKey: string,
@@ -363,8 +368,6 @@ class InternalBuilder {
         let subQuery = mainKnex
           .select(mainKnex.raw(1))
           .from({ [toAlias]: relatedTableName })
-          // relationships should never have more than the base limit
-          .limit(getBaseLimit())
         let mainTableRelatesTo = toAlias
         if (relationship.through) {
           const throughAlias =
@@ -375,12 +378,15 @@ class InternalBuilder {
           })
           subQuery = subQuery.innerJoin(throughTable, function () {
             // @ts-ignore
-            this.orOn(
+            this.on(
               `${toAlias}.${relationship.toPrimary}`,
               "=",
               `${throughAlias}.${relationship.to}`
             )
           })
+          if (this.client === SqlClient.SQL_LITE) {
+            subQuery = this.addJoinFieldCheck(subQuery, relationship)
+          }
           mainTableRelatesTo = throughAlias
         }
         // "join" to the main table, making sure the ID matches that of the main
@@ -907,7 +913,7 @@ class InternalBuilder {
         default:
           throw new Error(`JSON relationships not implement for ${this.client}`)
       }
-      const subQuery = this.knex
+      let subQuery = this.knex
         .select(rawJsonArray)
         .from(toTableWithSchema)
         .join(throughTableWithSchema, function () {
@@ -918,6 +924,12 @@ class InternalBuilder {
           "=",
           this.knex.raw(this.quotedIdentifier(`${fromAlias}.${fromPrimary}`))
         )
+        // relationships should never have more than the base limit
+        .limit(getBaseLimit())
+      // need to check the junction table document is to the right column
+      if (this.client === SqlClient.SQL_LITE) {
+        subQuery = this.addJoinFieldCheck(subQuery, relationship)
+      }
       query = query.select({ [relationship.column]: subQuery })
     }
     return query
diff --git a/packages/server/src/api/routes/tests/search.spec.ts b/packages/server/src/api/routes/tests/search.spec.ts
index bac9b6f774..44fe18d0ef 100644
--- a/packages/server/src/api/routes/tests/search.spec.ts
+++ b/packages/server/src/api/routes/tests/search.spec.ts
@@ -2687,7 +2687,8 @@ describe.each([
       })
     })
 
-  isSql &&
+  // TODO: when all SQL databases use the same mechanism - remove this test, new relationship system doesn't have this problem
+  !isInternal &&
     describe("pagination edge case with relationships", () => {
       let mainRows: Row[] = []
 
diff --git a/packages/server/src/utilities/rowProcessor/index.ts b/packages/server/src/utilities/rowProcessor/index.ts
index 795f6970ab..6028b2d248 100644
--- a/packages/server/src/utilities/rowProcessor/index.ts
+++ b/packages/server/src/utilities/rowProcessor/index.ts
@@ -336,6 +336,13 @@ export async function outputProcessing<T extends Row[] | Row>(
           row[property] = `${hours}:${minutes}:${seconds}`
         }
       }
+    } else if (column.type === FieldType.LINK) {
+      for (let row of enriched) {
+        // if relationship is empty - remove the array, this has been part of the API for some time
+        if (Array.isArray(row[property]) && row[property].length === 0) {
+          delete row[property]
+        }
+      }
     }
   }