diff --git a/src/Utilities/TrackedDependencies/CanonicalTrackedInputFiles.cs b/src/Utilities/TrackedDependencies/CanonicalTrackedInputFiles.cs
index a6281533708..be7d6f571f5 100644
--- a/src/Utilities/TrackedDependencies/CanonicalTrackedInputFiles.cs
+++ b/src/Utilities/TrackedDependencies/CanonicalTrackedInputFiles.cs
@@ -1033,6 +1033,9 @@ private void RemoveDependencyFromEntry(string rootingMarker, ITaskItem dependenc
         /// <param name="correspondingOutputs">Outputs that correspond ot the sources (used for same file processing)</param>
         public void RemoveDependenciesFromEntryIfMissing(ITaskItem[] source, ITaskItem[] correspondingOutputs)
         {
+            // Cache of files that have been checked and exist.
+            Dictionary<string, bool> fileCache = new Dictionary<string, bool>(StringComparer.OrdinalIgnoreCase);
+
             if (correspondingOutputs != null)
             {
                 ErrorUtilities.VerifyThrowArgument(source.Length == correspondingOutputs.Length, "Tracking_SourcesAndCorrespondingOutputMismatch");
@@ -1041,7 +1044,7 @@ public void RemoveDependenciesFromEntryIfMissing(ITaskItem[] source, ITaskItem[]
             // construct a combined root marker for the sources and outputs to remove from the graph
             string rootingMarker = FileTracker.FormatRootingMarker(source, correspondingOutputs);
 
-            RemoveDependenciesFromEntryIfMissing(rootingMarker);
+            RemoveDependenciesFromEntryIfMissing(rootingMarker, fileCache);
 
             // Remove entries for each individual source
             for (int sourceIndex = 0; sourceIndex < source.Length; sourceIndex++)
@@ -1049,7 +1052,7 @@ public void RemoveDependenciesFromEntryIfMissing(ITaskItem[] source, ITaskItem[]
                 rootingMarker = correspondingOutputs != null
                     ? FileTracker.FormatRootingMarker(source[sourceIndex], correspondingOutputs[sourceIndex])
                     : FileTracker.FormatRootingMarker(source[sourceIndex]);
-                RemoveDependenciesFromEntryIfMissing(rootingMarker);
+                RemoveDependenciesFromEntryIfMissing(rootingMarker, fileCache);
             }
         }
 
@@ -1057,7 +1060,8 @@ public void RemoveDependenciesFromEntryIfMissing(ITaskItem[] source, ITaskItem[]
         /// Remove the output graph entries for the given rooting marker
         /// </summary>
         /// <param name="rootingMarker"></param>
-        private void RemoveDependenciesFromEntryIfMissing(string rootingMarker)
+        /// <param name="fileCache">The cache used to store whether each file exists or not.</param>
+        private void RemoveDependenciesFromEntryIfMissing(string rootingMarker, Dictionary<string, bool> fileCache)
         {
             // In the event of incomplete tracking information (i.e. this root was not present), just continue quietly
             // as the user could have killed the tool being tracked, or another error occurred during its execution.
@@ -1070,8 +1074,19 @@ private void RemoveDependenciesFromEntryIfMissing(string rootingMarker)
                 {
                     if (keyIndex++ > 0)
                     {
-                        // If we are ignoring missing files, then only record those that exist
-                        if (FileUtilities.FileExistsNoThrow(file))
+                        // Record whether or not each file exists and cache it.
+                        // We do this to save time (On^2), at the expense of data O(n).
+                        bool inFileCache = fileCache.TryGetValue(file, out bool fileExists);
+
+                        // Have we cached the file yet? If not, cache whether or not it exists.
+                        if (!inFileCache)
+                        {
+                            fileExists = FileUtilities.FileExistsNoThrow(file);
+                            fileCache.Add(file, fileExists);
+                        }
+
+                        // Does the cached file exist?
+                        if (fileExists)
                         {
                             dependenciesWithoutMissingFiles.Add(file, dependencies[file]);
                         }
diff --git a/src/Utilities/TrackedDependencies/CanonicalTrackedOutputFiles.cs b/src/Utilities/TrackedDependencies/CanonicalTrackedOutputFiles.cs
index 5c906de1683..7ca96f897c0 100644
--- a/src/Utilities/TrackedDependencies/CanonicalTrackedOutputFiles.cs
+++ b/src/Utilities/TrackedDependencies/CanonicalTrackedOutputFiles.cs
@@ -724,6 +724,9 @@ private void RemoveDependencyFromEntry(string rootingMarker, ITaskItem dependenc
         /// <param name="correspondingOutputs">Outputs that correspond ot the sources (used for same file processing)</param>
         public void RemoveDependenciesFromEntryIfMissing(ITaskItem[] source, ITaskItem[] correspondingOutputs)
         {
+            // Cache of files and whether or not they exist.
+            Dictionary<string, bool> fileCache = new Dictionary<string, bool>(StringComparer.OrdinalIgnoreCase);
+
             if (correspondingOutputs != null)
             {
                 ErrorUtilities.VerifyThrowArgument(source.Length == correspondingOutputs.Length, "Tracking_SourcesAndCorrespondingOutputMismatch");
@@ -732,21 +735,15 @@ public void RemoveDependenciesFromEntryIfMissing(ITaskItem[] source, ITaskItem[]
             // construct a combined root marker for the sources and outputs to remove from the graph
             string rootingMarker = FileTracker.FormatRootingMarker(source, correspondingOutputs);
 
-            RemoveDependenciesFromEntryIfMissing(rootingMarker);
+            RemoveDependenciesFromEntryIfMissing(rootingMarker, fileCache);
 
             // Remove entries for each individual source
             for (int sourceIndex = 0; sourceIndex < source.Length; sourceIndex++)
             {
-                if (correspondingOutputs != null)
-                {
-                    rootingMarker = FileTracker.FormatRootingMarker(source[sourceIndex], correspondingOutputs[sourceIndex]);
-                }
-                else
-                {
-                    rootingMarker = FileTracker.FormatRootingMarker(source[sourceIndex]);
-                }
-
-                RemoveDependenciesFromEntryIfMissing(rootingMarker);
+                rootingMarker = correspondingOutputs != null
+                    ? FileTracker.FormatRootingMarker(source[sourceIndex], correspondingOutputs[sourceIndex])
+                    : FileTracker.FormatRootingMarker(source[sourceIndex]);
+                RemoveDependenciesFromEntryIfMissing(rootingMarker, fileCache);
             }
         }
 
@@ -754,7 +751,8 @@ public void RemoveDependenciesFromEntryIfMissing(ITaskItem[] source, ITaskItem[]
         /// Remove the output graph entries for the given rooting marker
         /// </summary>
         /// <param name="rootingMarker"></param>
-        private void RemoveDependenciesFromEntryIfMissing(string rootingMarker)
+        /// <param name="fileCache">The cache used to store whether each file exists or not.</param>
+        private void RemoveDependenciesFromEntryIfMissing(string rootingMarker, Dictionary<string, bool> fileCache)
         {
             // In the event of incomplete tracking information (i.e. this root was not present), just continue quietly
             // as the user could have killed the tool being tracked, or another error occurred during its execution.
@@ -767,8 +765,19 @@ private void RemoveDependenciesFromEntryIfMissing(string rootingMarker)
                 {
                     if (keyIndex++ > 0)
                     {
-                        // If we are ignoring missing files, then only record those that exist
-                        if (FileUtilities.FileExistsNoThrow(file))
+                        // Record whether or not each file exists and cache it.
+                        // We do this to save time (On^2), at the expense of data O(n).
+                        bool inFileCache = fileCache.TryGetValue(file, out bool fileExists);
+
+                        // Have we cached the file yet? If not, cache its existence.
+                        if (!inFileCache)
+                        {
+                            fileExists = FileUtilities.FileExistsNoThrow(file);
+                            fileCache.Add(file, fileExists);
+                        }
+
+                        // Does the cached file exist?
+                        if (fileExists)
                         {
                             dependenciesWithoutMissingFiles.Add(file, dependencies[file]);
                         }