diff --git a/OpenMcdf.Tests/RootStorageTests.cs b/OpenMcdf.Tests/RootStorageTests.cs
index 190c570..521eca8 100644
--- a/OpenMcdf.Tests/RootStorageTests.cs
+++ b/OpenMcdf.Tests/RootStorageTests.cs
@@ -207,4 +207,28 @@ public void SwitchTransactedStream(Version version, int subStorageCount)
                 rootStorage.OpenStorage($"Test{i}");
         }
     }
+
+    [TestMethod]
+    [DataRow(false)]
+    [DataRow(true)]
+    public void DeleteTrimsBaseStream(bool consolidate)
+    {
+        using var rootStorage = RootStorage.CreateInMemory(Version.V3);
+        using (CfbStream stream = rootStorage.CreateStream("Test"))
+        {
+            byte[] buffer = TestData.CreateByteArray(4096);
+            stream.Write(buffer, 0, buffer.Length);
+        }
+
+        rootStorage.Flush(consolidate);
+
+        long originalLength = rootStorage.BaseStream.Length;
+
+        rootStorage.Delete("Test");
+        rootStorage.Flush(consolidate);
+
+        long newLength = rootStorage.BaseStream.Length;
+
+        Assert.IsTrue(originalLength > newLength);
+    }
 }
diff --git a/OpenMcdf/Fat.cs b/OpenMcdf/Fat.cs
index 1450920..92c8a94 100644
--- a/OpenMcdf/Fat.cs
+++ b/OpenMcdf/Fat.cs
@@ -141,6 +141,18 @@ public uint Add(FatEnumerator fatEnumerator, uint startIndex)
         return entry.Index;
     }
 
+    public Sector GetLastUsedSector()
+    {
+        uint lastUsedSectorIndex = uint.MaxValue;
+        foreach (FatEntry entry in this)
+        {
+            if (!entry.IsFree)
+                lastUsedSectorIndex = entry.Index;
+        }
+
+        return new(lastUsedSectorIndex, Context.SectorSize);
+    }
+
     public IEnumerator<FatEntry> GetEnumerator() => new FatEnumerator(Context.Fat);
 
     IEnumerator IEnumerable.GetEnumerator() => GetEnumerator();
diff --git a/OpenMcdf/RootContext.cs b/OpenMcdf/RootContext.cs
index 0e88f63..b066534 100644
--- a/OpenMcdf/RootContext.cs
+++ b/OpenMcdf/RootContext.cs
@@ -87,8 +87,6 @@ public FatStream MiniStream
 
     public uint SectorCount => (uint)Math.Max(0, (Length - SectorSize) / SectorSize); // TODO: Check
 
-    bool isDirty;
-
     public RootContext(RootContextSite rootContextSite, Stream stream, Version version, IOContextFlags contextFlags = IOContextFlags.None)
         : base(rootContextSite)
     {
@@ -178,12 +176,10 @@ public void Flush()
     {
         Fat.Flush();
 
-        if (isDirty && writer is not null && transactedStream is null)
+        if (writer is not null && transactedStream is null)
         {
-            // Ensure the stream is as long as expected
-            BaseStream.SetLength(Length);
+            TrimBaseStream();
             WriteHeader();
-            isDirty = false;
         }
     }
 
@@ -191,7 +187,16 @@ public void ExtendStreamLength(long length)
     {
         if (Length < length)
             Length = length;
-        isDirty = true;
+    }
+
+    void TrimBaseStream()
+    {
+        Sector lastUsedSector = Fat.GetLastUsedSector();
+        if (!lastUsedSector.IsValid)
+            throw new FileFormatException("Last used sector is invalid");
+
+        Length = lastUsedSector.EndPosition;
+        BaseStream.SetLength(Length);
     }
 
     public void WriteHeader()