diff --git a/src/helpers/assertVectorSearchFilterFieldsAreIndexed.ts b/src/helpers/assertVectorSearchFilterFieldsAreIndexed.ts
index a7db5912..3ef762b7 100644
--- a/src/helpers/assertVectorSearchFilterFieldsAreIndexed.ts
+++ b/src/helpers/assertVectorSearchFilterFieldsAreIndexed.ts
@@ -8,7 +8,9 @@ import { type CompositeLogger, LogId } from "../common/logger.js";
 // https://www.mongodb.com/docs/atlas/atlas-vector-search/vector-search-stage/#mongodb-vector-search-pre-filter
 const ALLOWED_LOGICAL_OPERATORS = ["$not", "$nor", "$and", "$or"];
 
-export type VectorSearchIndex = {
+export type SearchIndex = VectorSearchIndex | AtlasSearchIndex;
+
+type VectorSearchIndex = {
     name: string;
     latestDefinition: {
         fields: Array<
@@ -21,6 +23,13 @@ export type VectorSearchIndex = {
               }
         >;
     };
+    type: "vectorSearch";
+};
+
+type AtlasSearchIndex = {
+    name: string;
+    latestDefinition: unknown;
+    type: "search";
 };
 
 export function assertVectorSearchFilterFieldsAreIndexed({
@@ -28,12 +37,14 @@ export function assertVectorSearchFilterFieldsAreIndexed({
     pipeline,
     logger,
 }: {
-    searchIndexes: VectorSearchIndex[];
+    searchIndexes: SearchIndex[];
     pipeline: Record<string, unknown>[];
     logger: CompositeLogger;
 }): void {
-    const searchIndexesWithFilterFields = searchIndexes.reduce<Record<string, string[]>>(
-        (indexFieldMap, searchIndex) => {
+    const searchIndexesWithFilterFields = searchIndexes
+        // Ensure we only process vector search indexes and not lexical search ones
+        .filter((index) => index.type === "vectorSearch")
+        .reduce<Record<string, string[]>>((indexFieldMap, searchIndex) => {
             const filterFields = searchIndex.latestDefinition.fields
                 .map<string | undefined>((field) => {
                     return field.type === "filter" ? field.path : undefined;
@@ -42,9 +53,7 @@ export function assertVectorSearchFilterFieldsAreIndexed({
 
             indexFieldMap[searchIndex.name] = filterFields;
             return indexFieldMap;
-        },
-        {}
-    );
+        }, {});
     for (const stage of pipeline) {
         if ("$vectorSearch" in stage) {
             const { $vectorSearch: vectorSearchStage } = stage as z.infer<typeof VectorSearchStage>;
diff --git a/src/tools/mongodb/read/aggregate.ts b/src/tools/mongodb/read/aggregate.ts
index 4ef641b4..c7bd439a 100644
--- a/src/tools/mongodb/read/aggregate.ts
+++ b/src/tools/mongodb/read/aggregate.ts
@@ -15,7 +15,7 @@ import { LogId } from "../../../common/logger.js";
 import { AnyAggregateStage, VectorSearchStage } from "../mongodbSchemas.js";
 import {
     assertVectorSearchFilterFieldsAreIndexed,
-    type VectorSearchIndex,
+    type SearchIndex,
 } from "../../../helpers/assertVectorSearchFilterFieldsAreIndexed.js";
 
 const pipelineDescriptionWithVectorSearch = `\
@@ -66,7 +66,7 @@ export class AggregateTool extends MongoDBToolBase {
             await this.assertOnlyUsesPermittedStages(pipeline);
             if (await this.session.isSearchSupported()) {
                 assertVectorSearchFilterFieldsAreIndexed({
-                    searchIndexes: (await provider.getSearchIndexes(database, collection)) as VectorSearchIndex[],
+                    searchIndexes: (await provider.getSearchIndexes(database, collection)) as SearchIndex[],
                     pipeline,
                     logger: this.session.logger,
                 });
diff --git a/tests/unit/helpers/assertVectorSearchFilterFieldsAreIndexed.test.ts b/tests/unit/helpers/assertVectorSearchFilterFieldsAreIndexed.test.ts
index a437a916..422c983c 100644
--- a/tests/unit/helpers/assertVectorSearchFilterFieldsAreIndexed.test.ts
+++ b/tests/unit/helpers/assertVectorSearchFilterFieldsAreIndexed.test.ts
@@ -2,7 +2,7 @@ import { describe, expect, it, vi } from "vitest";
 import {
     assertVectorSearchFilterFieldsAreIndexed,
     collectFieldsFromVectorSearchFilter,
-    type VectorSearchIndex,
+    type SearchIndex,
 } from "../../../src/helpers/assertVectorSearchFilterFieldsAreIndexed.js";
 import { ErrorCodes, MongoDBError } from "../../../src/common/errors.js";
 import { type CompositeLogger, LogId } from "../../../src/common/logger.js";
@@ -184,7 +184,7 @@ describe("#assertVectorSearchFilterFieldsAreIndexed", () => {
         error: vi.fn(),
     } as unknown as CompositeLogger;
 
-    const createMockSearchIndexes = (indexName: string, filterFields: string[]): VectorSearchIndex[] => [
+    const createMockSearchIndexes = (indexName: string, filterFields: string[]): SearchIndex[] => [
         {
             name: indexName,
             latestDefinition: {
@@ -196,6 +196,7 @@ describe("#assertVectorSearchFilterFieldsAreIndexed", () => {
                     })),
                 ],
             },
+            type: "vectorSearch",
         },
     ];
 
@@ -547,12 +548,13 @@ describe("#assertVectorSearchFilterFieldsAreIndexed", () => {
     });
 
     it("should handle search index with no filter fields", () => {
-        const searchIndexes: VectorSearchIndex[] = [
+        const searchIndexes: SearchIndex[] = [
             {
                 name: "myIndex",
                 latestDefinition: {
                     fields: [{ type: "vector" }],
                 },
+                type: "vectorSearch",
             },
         ];
         const pipeline = [
@@ -583,4 +585,45 @@ describe("#assertVectorSearchFilterFieldsAreIndexed", () => {
             )
         );
     });
+
+    it("should ignore atlas search indexes", () => {
+        const searchIndexes: SearchIndex[] = [
+            ...createMockSearchIndexes("index1", ["field1", "field2"]),
+            // Atlas search index - it should be ignored by the validation
+            // and not cause any errors
+            {
+                name: "atlasSearchIndex",
+                latestDefinition: {
+                    analyzer: "lucene.standard",
+                    mappings: {
+                        dynamic: false,
+                    },
+                },
+                type: "search",
+            },
+        ];
+
+        const pipeline = [
+            {
+                $vectorSearch: {
+                    index: "index1",
+                    path: "embedding",
+                    queryVector: [1, 2, 3],
+                    numCandidates: 100,
+                    limit: 10,
+                    filter: {
+                        field1: "value",
+                    },
+                },
+            },
+        ];
+
+        expect(() =>
+            assertVectorSearchFilterFieldsAreIndexed({
+                searchIndexes: searchIndexes,
+                pipeline,
+                logger: mockLogger,
+            })
+        ).not.toThrow();
+    });
 });