diff --git a/fastcov.py b/fastcov.py
index 30d013d..dbf719b 100755
--- a/fastcov.py
+++ b/fastcov.py
@@ -155,38 +155,45 @@ def processGcdas(args, coverage_files, gcov_filter_options):
 
     return base_fastcov
 
-def processGcov(cwd, gcov, files, gcov_filter_options):
-    # Add absolute path
-    gcov["file_abs"] = os.path.abspath(os.path.join(cwd, gcov["file"]))
-
+def shouldFilterSource(source, gcov_filter_options):
+    """Returns true if the provided source file should be filtered due to CLI options, otherwise returns false"""
     # If explicit sources were passed, check for match
     if gcov_filter_options["sources"]:
-        if gcov["file_abs"] in gcov_filter_options["sources"]:
-            files.append(gcov)
-            logging.debug("Accepted coverage for '%s'", gcov["file_abs"])
-        else:
-            logging.debug("Skipping coverage for '%s' due to option '--source-files'", gcov["file_abs"])
-        return
+        if source not in gcov_filter_options["sources"]:
+            logging.debug("Filtering coverage for '%s' due to option '--source-files'", source)
+            return True
 
     # Check exclude filter
     for ex in gcov_filter_options["exclude"]:
-        if ex in gcov["file_abs"]:
-            logging.debug("Skipping coverage for '%s' due to option '--exclude %s'", gcov["file_abs"], ex)
-            return
+        if ex in source:
+            logging.debug("Filtering coverage for '%s' due to option '--exclude %s'", source, ex)
+            return True
 
     # Check include filter
     if gcov_filter_options["include"]:
         included = False
-        for ex in gcov_filter_options["include"]:
-            if ex in gcov["file_abs"]:
+        for inc in gcov_filter_options["include"]:
+            if inc in source:
                 included = True
-                files.append(gcov)
-                logging.debug("Accepted coverage for '%s'", gcov["file_abs"])
                 break
 
         if not included:
-            logging.debug("Skipping coverage for '%s' due to option '--include %s'", gcov["file_abs"], " ".join(gcov_filter_options["include"]))
+            logging.debug("Filtering coverage for '%s' due to option '--include %s'", source, " ".join(gcov_filter_options["include"]))
+            return True
+
+    return False
+
+def filterFastcov(fastcov_json, args):
+    gcov_filter_options = getGcovFilterOptions(args)
+    for source in list(fastcov_json["sources"].keys()):
+        if shouldFilterSource(source, gcov_filter_options):
+            del fastcov_json["sources"][source]
+
+def processGcov(cwd, gcov, files, gcov_filter_options):
+    # Add absolute path
+    gcov["file_abs"] = os.path.abspath(os.path.join(cwd, gcov["file"]))
 
+    if shouldFilterSource(gcov["file_abs"], gcov_filter_options):
         return
 
     files.append(gcov)
@@ -544,6 +551,7 @@ def parseAndCombine(paths):
 def combineCoverageFiles(args):
     logging.info("Performing combine operation")
     fastcov_json = parseAndCombine(args.combine)
+    filterFastcov(fastcov_json, args)
     dumpFile(fastcov_json, args)
 
 def dumpFile(fastcov_json, args):
diff --git a/test/functional/expected_results/basic.fastcov.expected.json b/test/functional/expected_results/basic.fastcov.expected.json
new file mode 100644
index 0000000..aaeea78
--- /dev/null
+++ b/test/functional/expected_results/basic.fastcov.expected.json
@@ -0,0 +1,41 @@
+{
+    "sources": {
+        "/mnt/workspace/test/functional/cmake_project/src/source2.cpp": {
+            "": {
+                "functions": {
+                    "_Z3barbii": {
+                        "start_line": 3,
+                        "execution_count": 10
+                    }
+                },
+                "branches": {},
+                "lines": {
+                    "3": 10,
+                    "5": 10,
+                    "6": 10,
+                    "8": 0
+                }
+            }
+        },
+        "/mnt/workspace/test/functional/cmake_project/src/source1.cpp": {
+            "": {
+                "functions": {
+                    "_Z3foob": {
+                        "start_line": 3,
+                        "execution_count": 1
+                    }
+                },
+                "branches": {},
+                "lines": {
+                    "3": 1,
+                    "5": 1,
+                    "7": 1001,
+                    "8": 1000,
+                    "10": 1000,
+                    "11": 0,
+                    "14": 1
+                }
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/functional/run_all.sh b/test/functional/run_all.sh
index 43f7e9f..c9d211c 100755
--- a/test/functional/run_all.sh
+++ b/test/functional/run_all.sh
@@ -36,6 +36,9 @@ test `find . -name *.gcda | wc -l` -eq 0
 ${TEST_DIR}/fastcov.py --gcov gcov-9 --zerocounters  # Clear previous test coverage
 ctest -R ctest_1
 
+# Create a fastcov JSON to be filtered later
+coverage run -a ${TEST_DIR}/fastcov.py --gcov gcov-9 --verbose -o basic.fastcov.json
+
 # Test (basic report generation - no branches)
 coverage run -a ${TEST_DIR}/fastcov.py --gcov gcov-9 --verbose --exclude cmake_project/test/ --lcov -o test1.actual.info
 cmp test1.actual.info ${TEST_DIR}/expected_results/test1.expected.info
@@ -80,6 +83,16 @@ if coverage run -a ${TEST_DIR}/fastcov.py --gcov ${TEST_DIR}/fake-gcov.sh ; then
     exit 1
 fi
 
+# Combine operation - filtering
+coverage run -a ${TEST_DIR}/fastcov.py -C basic.fastcov.json --exclude cmake_project/test/ -o basic.fastcov.actual.json
+${TEST_DIR}/json_cmp.py basic.fastcov.actual.json ${TEST_DIR}/expected_results/basic.fastcov.expected.json
+
+coverage run -a ${TEST_DIR}/fastcov.py -C basic.fastcov.json --include cmake_project/src/ -o basic.fastcov2.actual.json
+${TEST_DIR}/json_cmp.py basic.fastcov2.actual.json ${TEST_DIR}/expected_results/basic.fastcov.expected.json
+
+coverage run -a ${TEST_DIR}/fastcov.py -C basic.fastcov.json --source-files /mnt/workspace/test/functional/cmake_project/src/source2.cpp /mnt/workspace/test/functional/cmake_project/src/source1.cpp -o basic.fastcov3.actual.json
+${TEST_DIR}/json_cmp.py basic.fastcov3.actual.json ${TEST_DIR}/expected_results/basic.fastcov.expected.json
+
 # Combine operation
 coverage run -a ${TEST_DIR}/fastcov.py -C ${TEST_DIR}/expected_results/test2.expected.info ${TEST_DIR}/expected_results/test1.tn.expected.info --lcov -o combine1.actual.info
 cmp combine1.actual.info ${TEST_DIR}/expected_results/combine1.expected.info