diff --git a/e2e/fixtures/samples/config-dev.json b/e2e/fixtures/samples/configs/config-dev.json
similarity index 100%
rename from e2e/fixtures/samples/config-dev.json
rename to e2e/fixtures/samples/configs/config-dev.json
diff --git a/e2e/fixtures/samples/configs/config-dev.yaml b/e2e/fixtures/samples/configs/config-dev.yaml
new file mode 100644
index 00000000000..19209d1b879
--- /dev/null
+++ b/e2e/fixtures/samples/configs/config-dev.yaml
@@ -0,0 +1,3 @@
+path: fixtures/samples/positive.dockerfile
+queries-path: ../assets/queries
+timeout: 12
diff --git a/e2e/fixtures/samples/config.json b/e2e/fixtures/samples/configs/config.json
similarity index 100%
rename from e2e/fixtures/samples/config.json
rename to e2e/fixtures/samples/configs/config.json
diff --git a/e2e/fixtures/samples/configs/config.yaml b/e2e/fixtures/samples/configs/config.yaml
new file mode 100644
index 00000000000..c209f2dd8ba
--- /dev/null
+++ b/e2e/fixtures/samples/configs/config.yaml
@@ -0,0 +1,3 @@
+path: /path/e2e/fixtures/samples/positive.dockerfile
+queries-path: /path/assets/queries
+timeout: 12
diff --git a/e2e/testcases/e2e-cli-029_scan_config.go b/e2e/testcases/e2e-cli-029_scan_config.go
index 8c38bb85835..d4c0457fea7 100644
--- a/e2e/testcases/e2e-cli-029_scan_config.go
+++ b/e2e/testcases/e2e-cli-029_scan_config.go
@@ -7,11 +7,11 @@ func init() { //nolint
 		Name: "should load a config file [E2E-CLI-029]",
 		Args: args{
 			Args: []cmdArgs{
-				[]string{"scan", "--config", "/path/e2e/fixtures/samples/config.json", "--type", "cloudformation"},
+				[]string{"scan", "--config", "/path/e2e/fixtures/samples/configs/config.json", "--type", "cloudformation"},
 
-				[]string{"scan", "--config", "/path/e2e/fixtures/samples/config.json"},
+				[]string{"scan", "--config", "/path/e2e/fixtures/samples/configs/config.json"},
 
-				[]string{"scan", "--config", "/path/e2e/fixtures/samples/config.json", "--silent"},
+				[]string{"scan", "--config", "/path/e2e/fixtures/samples/configs/config.json", "--silent"},
 			},
 		},
 		WantStatus: []int{50, 0, 126},
diff --git a/e2e/testcases/e2e-cli-056_scan_timeout.go b/e2e/testcases/e2e-cli-056_scan_timeout.go
new file mode 100644
index 00000000000..0095f8f3cae
--- /dev/null
+++ b/e2e/testcases/e2e-cli-056_scan_timeout.go
@@ -0,0 +1,27 @@
+package testcases
+
+import (
+	"regexp"
+)
+
+// E2E-CLI-056 - Kics scan command with timeout flag
+// should stop a query execution when reaching the provided timeout (seconds)
+func init() { //nolint
+	testSample := TestCase{
+		Name: "should timeout queries when reaching the timeout limit [E2E-CLI-056]",
+		Args: args{
+			Args: []cmdArgs{
+				[]string{"scan", "--config", "/path/e2e/fixtures/samples/configs/config.yaml", "-v"},
+				[]string{"scan", "-p", "/path/e2e/fixtures/samples/positive.dockerfile", "--timeout", "1", "-v"},
+				[]string{"scan", "-p", "/path/e2e/fixtures/samples/positive.dockerfile", "--timeout", "0", "-v"},
+			},
+		},
+		WantStatus: []int{50, 50, 126},
+		Validation: func(outputText string) bool {
+			matchTimeoutLog, _ := regexp.MatchString("Query execution timeout=(0|1|12)s", outputText)
+			return matchTimeoutLog
+		},
+	}
+
+	Tests = append(Tests, testSample)
+}
diff --git a/e2e/utils/helper.go b/e2e/utils/helper.go
index 9d9d3f9123d..1bac4b8b8ec 100644
--- a/e2e/utils/helper.go
+++ b/e2e/utils/helper.go
@@ -49,8 +49,11 @@ func RunCommand(kicsArgs []string, useDocker, useMock bool, kicsDockerImage stri
 
 // KicsDevPathAdapter adapts the path to enable kics locally execution
 func KicsDevPathAdapter(path string) string {
-	if path == "/path/e2e/fixtures/samples/config.json" {
+	// [e2e-029] and [e2e-056] config tests
+	if path == "/path/e2e/fixtures/samples/configs/config.json" {
 		path = strings.Replace(path, "config.json", "config-dev.json", -1)
+	} else if path == "/path/e2e/fixtures/samples/configs/config.yaml" {
+		path = strings.Replace(path, "config.yaml", "config-dev.yaml", -1)
 	}
 	regex := regexp.MustCompile(`/path/\w+/`)
 	matches := regex.FindString(path)
diff --git a/pkg/engine/secrets/inspector.go b/pkg/engine/secrets/inspector.go
index 1f2529735d4..896822eb5c7 100644
--- a/pkg/engine/secrets/inspector.go
+++ b/pkg/engine/secrets/inspector.go
@@ -163,7 +163,7 @@ func NewInspector(
 
 func (c *Inspector) inspectQuery(ctx context.Context, basePaths []string,
 	files model.FileMetadatas, i int) ([]model.Vulnerability, error) {
-	timeoutCtx, cancel := context.WithTimeout(ctx, c.queryExecutionTimeout*time.Second)
+	timeoutCtx, cancel := context.WithTimeout(ctx, c.queryExecutionTimeout)
 	defer cancel()
 
 	cleanFiles := cleanFiles(files)