diff --git a/src/N3Store.js b/src/N3Store.js
index 675b44f0..4bd66c3b 100644
--- a/src/N3Store.js
+++ b/src/N3Store.js
@@ -45,6 +45,40 @@ function intersect(s1, s2, depth = 4) {
   return target;
 }
 
+/**
+ * Determines the difference of the `_graphs` index s1 and s2.
+ * s1 and s2 *must* belong to Stores that share an `_entityIndex`.
+ *
+ * False is returned when there is no difference; this should
+ * *not* be set as the value for an index.
+ */
+function difference(s1, s2, depth = 4) {
+  let target = false;
+
+  for (const key in s1) {
+    // When the key is not in the index, then none of the triples defined by s1[key] are
+    // in s2 and so we want to copy them over to the resultant store.
+    if (!(key in s2)) {
+      target = target || Object.create(null);
+      target[key] = depth === 0 ? null : merge({}, s1[key], depth - 1);
+    }
+    else if (depth !== 0) {
+      const diff = difference(s1[key], s2[key], depth - 1);
+      if (diff !== false) {
+        target = target || Object.create(null);
+        target[key] = diff;
+      }
+      // Depth 3 is the 'subjects', 'predicates' and 'objects' keys.
+      // If the 'subjects' index is empty, so will the 'predicates' and 'objects' index.
+      else if (depth === 3) {
+        return false;
+      }
+    }
+  }
+
+  return target;
+}
+
 // ## Constructor
 export class N3EntityIndex {
   constructor(options = {}) {
@@ -896,6 +930,16 @@ export default class N3Store {
     if (other === this)
       return new N3Store({ entityIndex: this._entityIndex });
 
+    if ((other instanceof N3Store) && other._entityIndex === this._entityIndex) {
+      const store = new N3Store({ entityIndex: this._entityIndex });
+      const graphs = difference(this._graphs, other._graphs);
+      if (graphs) {
+        store._graphs = graphs;
+        store._size = null;
+      }
+      return store;
+    }
+
     return this.filter(quad => !other.has(quad));
   }
 
diff --git a/test/N3Store-test.js b/test/N3Store-test.js
index 2945687a..210c2ee7 100644
--- a/test/N3Store-test.js
+++ b/test/N3Store-test.js
@@ -2139,6 +2139,25 @@ describe('Store', () => {
 
         expect(store.difference(store).size).toEqual(0);
         expect(store2.difference(store2).size).toEqual(0);
+        expect(store.difference(new Store([...store])).size).toEqual(0);
+        expect(store2.difference(new Store([...store2])).size).toEqual(0);
+
+        const stores = [store, store1, store2, store3, store4, storeb, storeg, empty];
+        for (const s1 of stores) {
+          for (const s2 of stores) {
+            expect(s1.difference(s2).size).toBeLessThanOrEqual(s1.size);
+            expect(s1.difference(s2)._graphs).toBeTruthy();
+            expect(s1.union(s2).difference(s1).equals(s2.difference(s1))).toBe(true);
+            expect(s1.difference(s2).union(s1).equals(s1)).toBe(true);
+            expect(new Store([...s1.union(s2).difference(s1)]).equals(new Store([...s2.difference(s1)]))).toBe(true);
+            expect(new Store([...s1.difference(s2).union(s1)]).equals(new Store([...s1]))).toBe(true);
+
+            const newStore = s1.difference(s2);
+            const size = newStore.size;
+            newStore.add(new Quad(new NamedNode('mys1'), new NamedNode('myp1'), new NamedNode('myo1')));
+            expect(newStore.size).toBe(size + 1);
+          }
+        }
       });
     });