diff --git a/cmd/uptest/main.go b/cmd/uptest/main.go
index 508592d..a3d2547 100644
--- a/cmd/uptest/main.go
+++ b/cmd/uptest/main.go
@@ -45,6 +45,8 @@ var (
 	renderOnly         = e2e.Flag("render-only", "Only render test files. Do not run the tests.").Default("false").Bool()
 	logCollectInterval = e2e.Flag("log-collect-interval", "Specifies the interval duration for collecting logs. "+
 		"The duration should be provided in a format understood by the tool, such as seconds (s), minutes (m), or hours (h). For example, '30s' for 30 seconds, '5m' for 5 minutes, or '1h' for one hour.").Default("30s").Duration()
+	skipUpdate = e2e.Flag("skip-update", "Skip the update step of the test.").Default("false").Bool()
+	skipImport = e2e.Flag("skip-import", "Skip the import step of the test.").Default("false").Bool()
 )
 
 func main() {
@@ -95,6 +97,8 @@ func e2eTests() {
 		DefaultTimeout:           *defaultTimeout,
 		Directory:                *testDir,
 		SkipDelete:               *skipDelete,
+		SkipUpdate:               *skipUpdate,
+		SkipImport:               *skipImport,
 		OnlyCleanUptestResources: *onlyCleanUptestResources,
 		RenderOnly:               *renderOnly,
 		LogCollectionInterval:    *logCollectInterval,
diff --git a/internal/config/config.go b/internal/config/config.go
index 15e5424..ff774b2 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -55,6 +55,8 @@ type AutomatedTest struct {
 	DefaultConditions []string
 
 	SkipDelete bool
+	SkipUpdate bool
+	SkipImport bool
 
 	OnlyCleanUptestResources bool
 
diff --git a/internal/tester.go b/internal/tester.go
index 88d9bd4..e03a314 100644
--- a/internal/tester.go
+++ b/internal/tester.go
@@ -32,6 +32,8 @@ var testFiles = []string{
 	"03-delete.yaml",
 }
 
+const crossplaneTempError = "crossplane: error: cannot get requested resource"
+
 func newTester(ms []config.Manifest, opts *config.AutomatedTest) *tester {
 	return &tester{
 		options:   opts,
@@ -122,14 +124,19 @@ func logCollector(done chan bool, ticker *time.Ticker, mutex sync.Locker, resour
 			return
 		case <-ticker.C:
 			mutex.Lock()
-			log.Printf("crossplane trace logs %s\n", time.Now())
 			for _, r := range resources {
 				traceCmd := exec.Command("bash", "-c", fmt.Sprintf(`"${CROSSPLANE_CLI}" beta trace %s %s -o wide`, r.KindGroup, r.Name)) //nolint:gosec // Disabling gosec to allow dynamic shell command execution
 				output, err := traceCmd.CombinedOutput()
 				if err != nil {
-					log.Println("Error executing crossplane:", err)
+					// During the setup script is running, the crossplane command
+					// is failing because of the resource not found error.
+					// We do not want to show this error to the user because it
+					// is a noise and temporary one.
+					if !strings.Contains(string(output), crossplaneTempError) {
+						log.Printf("crossplane trace logs %s\n%s: %s: %s\n", time.Now(), "Error executing crossplane", err, string(output))
+					}
 				} else {
-					log.Println(string(output))
+					log.Printf("crossplane trace logs %s\n%s\n", time.Now(), string(output))
 				}
 			}
 			mutex.Unlock()
@@ -148,6 +155,7 @@ func (t *tester) prepareConfig() (*config.TestCase, []config.Resource, error) {
 	}
 	examples := make([]config.Resource, 0, len(t.manifests))
 
+	rootFound := false
 	for _, m := range t.manifests {
 		obj := m.Object
 		groupVersionKind := obj.GroupVersionKind()
@@ -238,12 +246,26 @@ func (t *tester) prepareConfig() (*config.TestCase, []config.Resource, error) {
 					tc.SkipUpdate = true
 				}
 				example.Root = true
+				rootFound = true
 			}
 		}
 
 		examples = append(examples, example)
 	}
 
+	if !rootFound {
+		log.Println("Skipping update step because the root resource does not exist")
+		tc.SkipUpdate = true
+	}
+	if t.options.SkipUpdate {
+		log.Println("Skipping update step because the skip-delete option is set to true")
+		tc.SkipUpdate = true
+	}
+	if t.options.SkipImport {
+		log.Println("Skipping import step because the skip-import option is set to true")
+		tc.SkipImport = true
+	}
+
 	return tc, examples, nil
 }