diff --git a/domain/src/main/scala/scoverage/domain/coverage.scala b/domain/src/main/scala/scoverage/domain/coverage.scala
index a6b8764c..86e59757 100644
--- a/domain/src/main/scala/scoverage/domain/coverage.scala
+++ b/domain/src/main/scala/scoverage/domain/coverage.scala
@@ -12,14 +12,23 @@ case class Coverage()
     with PackageBuilders
     with FileBuilders {
 
+  private var _maxId: Int = 0
   private val statementsById = mutable.Map[Int, Statement]()
   override def statements = statementsById.values
-  def add(stmt: Statement): Unit = statementsById.put(stmt.id, stmt)
-
+  def add(stmt: Statement): Unit = {
+    if (stmt.id > _maxId) {
+      _maxId = stmt.id
+    }
+    statementsById.put(stmt.id, stmt)
+  }
   private val ignoredStatementsById = mutable.Map[Int, Statement]()
   override def ignoredStatements = ignoredStatementsById.values
-  def addIgnoredStatement(stmt: Statement): Unit =
+  def addIgnoredStatement(stmt: Statement): Unit = {
+    if (stmt.id > _maxId) {
+      _maxId = stmt.id
+    }
     ignoredStatementsById.put(stmt.id, stmt)
+  }
 
   def avgClassesPerPackage = classCount / packageCount.toDouble
   def avgClassesPerPackageFormatted: String = DoubleFormat.twoFractionDigits(
@@ -46,6 +55,8 @@ case class Coverage()
   def apply(ids: Iterable[(Int, String)]): Unit = ids foreach invoked
   def invoked(id: (Int, String)): Unit =
     statementsById.get(id._1).foreach(_.invoked(id._2))
+
+  def maxId: Int = _maxId
 }
 
 trait ClassBuilders {
diff --git a/plugin/src/main/scala/scoverage/CoverageMerge.scala b/plugin/src/main/scala/scoverage/CoverageMerge.scala
new file mode 100644
index 00000000..4a9d6215
--- /dev/null
+++ b/plugin/src/main/scala/scoverage/CoverageMerge.scala
@@ -0,0 +1,27 @@
+package scoverage
+
+import java.io.File
+
+import scoverage.domain.Coverage
+
+object CoverageMerge {
+  def mergePreviousAndCurrentCoverage(
+      lastCompiledFiles: Set[String],
+      previousCoverage: Coverage,
+      currentCoverage: Coverage
+  ): Coverage = {
+    val mergedCoverage = Coverage()
+
+    previousCoverage.statements
+      .filterNot(stmt =>
+        lastCompiledFiles.contains(stmt.source) ||
+          !new File(stmt.source).exists()
+      )
+      .foreach { stmt =>
+        mergedCoverage.add(stmt)
+      }
+    currentCoverage.statements.foreach(stmt => mergedCoverage.add(stmt))
+
+    mergedCoverage
+  }
+}
diff --git a/plugin/src/main/scala/scoverage/ScoveragePlugin.scala b/plugin/src/main/scala/scoverage/ScoveragePlugin.scala
index bedc079d..90da4703 100644
--- a/plugin/src/main/scala/scoverage/ScoveragePlugin.scala
+++ b/plugin/src/main/scala/scoverage/ScoveragePlugin.scala
@@ -84,6 +84,7 @@ class ScoverageInstrumentationComponent(
 
   val statementIds = new AtomicInteger(0)
   val coverage = new Coverage
+  val compiledFiles = Set.newBuilder[String]
 
   override val phaseName: String = ScoveragePlugin.phaseName
   override val runsAfter: List[String] =
@@ -121,22 +122,39 @@ class ScoverageInstrumentationComponent(
   override def newPhase(prev: scala.tools.nsc.Phase): Phase = new Phase(prev) {
 
     override def run(): Unit = {
-      reporter.echo(s"Cleaning datadir [${options.dataDir}]")
-      // we clean the data directory, because if the code has changed, then the number / order of
-      // statements has changed by definition. So the old data would reference statements incorrectly
-      // and thus skew the results.
+      reporter.echo(
+        s"Cleaning measurements files in datadir [${options.dataDir}]"
+      )
       Serializer.clean(options.dataDir)
 
+      val coverageFile = Serializer.coverageFile(options.dataDir)
+      val sourceRootFile = new File(options.sourceRoot)
+      val previousCoverage =
+        if (coverageFile.exists())
+          Serializer.deserialize(
+            coverageFile,
+            sourceRootFile
+          )
+        else Coverage()
+
+      statementIds.set(previousCoverage.maxId)
+
       reporter.echo("Beginning coverage instrumentation")
       super.run()
       reporter.echo(
         s"Instrumentation completed [${coverage.statements.size} statements]"
       )
 
+      val mergedCoverage = CoverageMerge.mergePreviousAndCurrentCoverage(
+        lastCompiledFiles = compiledFiles.result(),
+        previousCoverage = previousCoverage,
+        currentCoverage = coverage
+      )
+
       Serializer.serialize(
-        coverage,
-        Serializer.coverageFile(options.dataDir),
-        new File(options.sourceRoot)
+        mergedCoverage,
+        coverageFile,
+        sourceRootFile
       )
       reporter.echo(
         s"Wrote instrumentation file [${Serializer.coverageFile(options.dataDir)}]"
@@ -153,6 +171,8 @@ class ScoverageInstrumentationComponent(
 
     import global._
 
+    compiledFiles += unit.source.file.absolute.canonicalPath
+
     // contains the location of the last node
     var location: domain.Location = _
 
diff --git a/plugin/src/test/scala/scoverage/IncrementalCoverageTest.scala b/plugin/src/test/scala/scoverage/IncrementalCoverageTest.scala
new file mode 100644
index 00000000..8e2688e1
--- /dev/null
+++ b/plugin/src/test/scala/scoverage/IncrementalCoverageTest.scala
@@ -0,0 +1,101 @@
+package scoverage
+
+import munit.FunSuite
+
+class IncrementalCoverageTest extends FunSuite {
+
+  case class Compilation(basePath: java.io.File, code: String) {
+    val coverageFile = serialize.Serializer.coverageFile(basePath)
+    val compiler = ScoverageCompiler(basePath = basePath)
+
+    val file = compiler.writeCodeSnippetToTempFile(code)
+    compiler.compileSourceFiles(file)
+    compiler.assertNoErrors()
+
+    val coverage = serialize.Serializer.deserialize(coverageFile, basePath)
+  }
+
+  test(
+    "should keep coverage from previous compilation when compiling incrementally"
+  ) {
+    val basePath = ScoverageCompiler.tempBasePath()
+
+    val compilation1 =
+      Compilation(basePath, """object First { def test(): Int = 42 }""")
+
+    locally {
+      val sourceFiles = compilation1.coverage.files.map(_.source).toSet
+      assertEquals(sourceFiles, Set(compilation1.file.getCanonicalPath))
+    }
+
+    val compilation2 =
+      Compilation(
+        basePath,
+        """object Second { def test(): String = "hello" }"""
+      )
+
+    locally {
+      val sourceFiles = compilation2.coverage.files.map(_.source).toSet
+      assertEquals(
+        sourceFiles,
+        Set(compilation1.file, compilation2.file).map(_.getCanonicalPath)
+      )
+    }
+  }
+
+  test(
+    "should not keep coverage from previous compilation if the source file was deleted"
+  ) {
+    val basePath = ScoverageCompiler.tempBasePath()
+
+    val compilation1 =
+      Compilation(basePath, """object First { def test(): Int = 42 }""")
+
+    locally {
+      val sourceFiles = compilation1.coverage.files.map(_.source).toSet
+
+      assertEquals(sourceFiles, Set(compilation1.file.getCanonicalPath))
+    }
+
+    compilation1.file.delete()
+
+    val compilation2 = Compilation(basePath, "")
+
+    locally {
+      val sourceFiles = compilation2.coverage.files.map(_.source).toSet
+      assertEquals(sourceFiles, Set.empty[String])
+    }
+  }
+
+  test(
+    "should not keep coverage from previous compilation if the source file was compiled again"
+  ) {
+    val basePath = ScoverageCompiler.tempBasePath()
+
+    val compilation1 =
+      Compilation(basePath, """object First { def test(): Int = 42 }""")
+
+    reporter.IOUtils.writeToFile(
+      compilation1.file,
+      """object Second { def test(): String = "hello" }""",
+      None
+    )
+
+    val coverageFile = serialize.Serializer.coverageFile(basePath)
+    val compiler = ScoverageCompiler(basePath = basePath)
+
+    compiler.compileSourceFiles(compilation1.file)
+    compiler.assertNoErrors()
+
+    val coverage = serialize.Serializer.deserialize(coverageFile, basePath)
+
+    locally {
+      val classNames = coverage.statements.map(_.location.className).toSet
+      assertEquals(
+        classNames,
+        Set("Second"),
+        s"First class should not be in coverage, but found: ${classNames.mkString(", ")}"
+      )
+    }
+  }
+}
diff --git a/plugin/src/test/scala/scoverage/ScoverageCompiler.scala b/plugin/src/test/scala/scoverage/ScoverageCompiler.scala
index 0f766474..f709f51e 100644
--- a/plugin/src/test/scala/scoverage/ScoverageCompiler.scala
+++ b/plugin/src/test/scala/scoverage/ScoverageCompiler.scala
@@ -3,6 +3,7 @@ package scoverage
 import java.io.File
 import java.io.FileNotFoundException
 import java.net.URL
+import java.util.UUID
 
 import scala.collection.mutable.ListBuffer
 import scala.tools.nsc.Global
@@ -55,20 +56,30 @@ private[scoverage] object ScoverageCompiler {
     s
   }
 
-  def default: ScoverageCompiler = {
-    val reporter = new scala.tools.nsc.reporters.ConsoleReporter(settings)
-    new ScoverageCompiler(settings, reporter, validatePositions = true)
+  def tempBasePath(): File =
+    new File(IOUtils.getTempPath, UUID.randomUUID.toString)
+
+  def apply(
+      settings: scala.tools.nsc.Settings = settings,
+      reporter: scala.tools.nsc.reporters.Reporter =
+        new scala.tools.nsc.reporters.ConsoleReporter(settings),
+      validatePositions: Boolean = true,
+      basePath: File = tempBasePath()
+  ) = {
+    new ScoverageCompiler(
+      settings,
+      reporter,
+      validatePositions,
+      basePath
+    )
   }
 
-  def noPositionValidation: ScoverageCompiler = {
-    val reporter = new scala.tools.nsc.reporters.ConsoleReporter(settings)
-    new ScoverageCompiler(settings, reporter, validatePositions = false)
-  }
+  def default = ScoverageCompiler()
 
-  def defaultJS: ScoverageCompiler = {
-    val reporter = new scala.tools.nsc.reporters.ConsoleReporter(jsSettings)
-    new ScoverageCompiler(jsSettings, reporter, validatePositions = true)
-  }
+  def noPositionValidation: ScoverageCompiler =
+    ScoverageCompiler(validatePositions = false)
+
+  def defaultJS: ScoverageCompiler = ScoverageCompiler(settings = jsSettings)
 
   def locationCompiler: LocationCompiler = {
     val reporter = new scala.tools.nsc.reporters.ConsoleReporter(settings)
@@ -158,7 +169,8 @@ private[scoverage] object ScoverageCompiler {
 class ScoverageCompiler(
     settings: scala.tools.nsc.Settings,
     rep: scala.tools.nsc.reporters.Reporter,
-    validatePositions: Boolean
+    validatePositions: Boolean,
+    basePath: File
 ) extends scala.tools.nsc.Global(settings, rep) {
 
   def addToClassPath(file: File): Unit = {
@@ -171,8 +183,8 @@ class ScoverageCompiler(
 
   val coverageOptions = ScoverageOptions
     .default()
-    .copy(dataDir = IOUtils.getTempPath)
-    .copy(sourceRoot = IOUtils.getTempPath)
+    .copy(dataDir = basePath.getAbsolutePath)
+    .copy(sourceRoot = basePath.getAbsolutePath)
 
   instrumentationComponent.setOptions(coverageOptions)
   val testStore = new ScoverageTestStoreComponent(this)
@@ -188,7 +200,7 @@ class ScoverageCompiler(
   }
 
   def writeCodeSnippetToTempFile(code: String): File = {
-    val file = File.createTempFile("scoverage_snippet", ".scala")
+    val file = File.createTempFile("scoverage_snippet", ".scala", basePath)
     IOUtils.writeToFile(file, code, None)
     file.deleteOnExit()
     file