diff --git a/index.js b/index.js
index 46c6d60c2..31fec4bbd 100755
--- a/index.js
+++ b/index.js
@@ -415,22 +415,22 @@ function coverageFinder () {
 }
 
 NYC.prototype.getCoverageMapFromAllCoverageFiles = function (baseDirectory) {
-  var _this = this
   var map = libCoverage.createCoverageMap({})
 
   this.eachReport(undefined, (report) => {
     map.merge(report)
   }, baseDirectory)
+
+  map.data = this.sourceMaps.remapCoverage(map.data)
+
   // depending on whether source-code is pre-instrumented
   // or instrumented using a JIT plugin like @babel/require
   // you may opt to exclude files after applying
   // source-map remapping logic.
   if (this.config.excludeAfterRemap) {
-    map.filter(function (filename) {
-      return _this.exclude.shouldInstrument(filename)
-    })
+    map.filter(filename => this.exclude.shouldInstrument(filename))
   }
-  map.data = this.sourceMaps.remapCoverage(map.data)
+
   return map
 }
 
diff --git a/test/nyc-integration.js b/test/nyc-integration.js
index 957b0c84b..3139bc346 100644
--- a/test/nyc-integration.js
+++ b/test/nyc-integration.js
@@ -1043,6 +1043,39 @@ describe('the nyc cli', function () {
           done()
         })
       })
+
+      it('uses source-maps to exclude original sources from reports', (done) => {
+        const args = [
+          bin,
+          '--all',
+          '--cache', 'false',
+          '--exclude', 'original/s1.js',
+          process.execPath, './instrumented/s1.min.js'
+        ]
+
+        const proc = spawn(process.execPath, args, {
+          cwd: fixturesSourceMaps,
+          env: env
+        })
+
+        var stdout = ''
+        proc.stdout.on('data', function (chunk) {
+          stdout += chunk
+        })
+
+        proc.on('close', function (code) {
+          code.should.equal(0)
+          stdoutShouldEqual(stdout, `
+            ----------|----------|----------|----------|----------|-------------------|
+            File      |  % Stmts | % Branch |  % Funcs |  % Lines | Uncovered Line #s |
+            ----------|----------|----------|----------|----------|-------------------|
+            All files |        0 |      100 |        0 |        0 |                   |
+             s2.js    |        0 |      100 |        0 |        0 |           1,2,4,6 |
+            ----------|----------|----------|----------|----------|-------------------|`
+          )
+          done()
+        })
+      })
     })
 
     describe('.map file', () => {