diff --git a/packages/gatsby/src/schema/__tests__/infer-graphql-input-type-test.js b/packages/gatsby/src/schema/__tests__/infer-graphql-input-type-test.js
index dd11b0e4448d9..aac4e6c5dd031 100644
--- a/packages/gatsby/src/schema/__tests__/infer-graphql-input-type-test.js
+++ b/packages/gatsby/src/schema/__tests__/infer-graphql-input-type-test.js
@@ -482,4 +482,33 @@ describe(`GraphQL Input args`, () => {
 
     expect(result).toMatchSnapshot()
   })
+
+  it(`filters on linked fields`, async () => {
+    const { store, getNodes } = require(`../../redux`)
+    const linkedNodeType = new GraphQLObjectType({
+      name: `Bar`,
+      fields: {
+        id: { type: GraphQLString },
+      },
+    })
+    let types = [{ name: `Bar`, nodeObjectType: linkedNodeType }]
+
+    store.dispatch({
+      type: `CREATE_NODE`,
+      payload: { id: `baz`, internal: { type: `Bar` } },
+    })
+
+    let result = await queryResult(
+      [...getNodes(), { linked___NODE: `baz`, foo: `bar` }],
+      `
+        {
+          allNode(filter: { linked: { id: { eq: "baz" } } }) {
+            edges { node { linked { id } } }
+          }
+        }
+      `,
+      { types }
+    )
+    expect(result.data.allNode.edges[0].node.linked.id).toEqual(`baz`)
+  })
 })
diff --git a/packages/gatsby/src/schema/infer-graphql-input-fields.js b/packages/gatsby/src/schema/infer-graphql-input-fields.js
index fea138023e433..df3f7d381e464 100644
--- a/packages/gatsby/src/schema/infer-graphql-input-fields.js
+++ b/packages/gatsby/src/schema/infer-graphql-input-fields.js
@@ -19,6 +19,8 @@ const {
   isEmptyObjectOrArray,
 } = require(`./data-tree-utils`)
 
+const { findLinkedNode } = require(`./infer-graphql-type`)
+
 import type {
   GraphQLInputFieldConfig,
   GraphQLInputFieldConfigMap,
@@ -202,7 +204,10 @@ export function inferInputObjectStructureFromNodes({
     if (isRoot && EXCLUDE_KEYS[key]) return
 
     // Input arguments on linked fields aren't currently supported
-    if (_.includes(key, `___NODE`)) return
+    if (_.includes(key, `___NODE`)) {
+      value = findLinkedNode(value)
+      ;[key] = key.split(`___`)
+    }
 
     let field = inferGraphQLInputFields({
       nodes,
diff --git a/packages/gatsby/src/schema/infer-graphql-type.js b/packages/gatsby/src/schema/infer-graphql-type.js
index 22a400c24031d..34b5bf75db102 100644
--- a/packages/gatsby/src/schema/infer-graphql-type.js
+++ b/packages/gatsby/src/schema/infer-graphql-type.js
@@ -252,7 +252,7 @@ function inferFromMapping(
   }
 }
 
-function findLinkedNode(value, linkedField, path) {
+export function findLinkedNode(value, linkedField, path) {
   let linkedNode
   // If the field doesn't link to the id, use that for searching.
   if (linkedField) {