diff --git a/cmd/run/run.go b/cmd/run/run.go
index 5668e06..f2c59e4 100644
--- a/cmd/run/run.go
+++ b/cmd/run/run.go
@@ -314,10 +314,6 @@ func NewRunCommand(cfg *command.Config) *cobra.Command {
 			}
 
 			mp := ModelParameters{}
-			err = mp.PopulateFromFlags(cmd.Flags())
-			if err != nil {
-				return err
-			}
 
 			if pf != nil {
 				mp.maxTokens = pf.ModelParameters.MaxTokens
@@ -325,6 +321,11 @@ func NewRunCommand(cfg *command.Config) *cobra.Command {
 				mp.topP = pf.ModelParameters.TopP
 			}
 
+			err = mp.PopulateFromFlags(cmd.Flags())
+			if err != nil {
+				return err
+			}
+
 			for {
 				prompt := ""
 				if initialPrompt != "" {
diff --git a/cmd/run/run_test.go b/cmd/run/run_test.go
index 27cc468..9a258ac 100644
--- a/cmd/run/run_test.go
+++ b/cmd/run/run_test.go
@@ -226,4 +226,108 @@ messages:
 
 		require.Contains(t, out.String(), reply)
 	})
+
+	t.Run("cli flags override params set in the prompt.yaml file", func(t *testing.T) {
+		// Begin setup:
+		const yamlBody = `
+    name: Example Prompt
+    description: Example description
+    model: openai/example-model
+    modelParameters:
+      maxTokens: 300
+      temperature: 0.8
+      topP: 0.9
+    messages:
+      - role: system
+        content: System message
+      - role: user
+        content: User message
+    `
+		tmp, err := os.CreateTemp(t.TempDir(), "*.prompt.yaml")
+		require.NoError(t, err)
+		_, err = tmp.WriteString(yamlBody)
+		require.NoError(t, err)
+		require.NoError(t, tmp.Close())
+
+		client := azuremodels.NewMockClient()
+		modelSummary := &azuremodels.ModelSummary{
+			Name:      "example-model",
+			Publisher: "openai",
+			Task:      "chat-completion",
+		}
+		modelSummary2 := &azuremodels.ModelSummary{
+			Name:      "example-model-4o-mini-plus",
+			Publisher: "openai",
+			Task:      "chat-completion",
+		}
+
+		client.MockListModels = func(ctx context.Context) ([]*azuremodels.
+			ModelSummary, error) {
+			return []*azuremodels.ModelSummary{modelSummary, modelSummary2}, nil
+		}
+
+		var capturedReq azuremodels.ChatCompletionOptions
+		reply := "hello"
+		chatCompletion := azuremodels.ChatCompletion{
+			Choices: []azuremodels.ChatChoice{{
+				Message: &azuremodels.ChatChoiceMessage{
+					Content: util.Ptr(reply),
+					Role:    util.Ptr(string(azuremodels.ChatMessageRoleAssistant)),
+				},
+			}},
+		}
+
+		client.MockGetChatCompletionStream = func(ctx context.Context, opt azuremodels.ChatCompletionOptions) (*azuremodels.ChatCompletionResponse, error) {
+			capturedReq = opt
+			return &azuremodels.ChatCompletionResponse{
+				Reader: sse.NewMockEventReader([]azuremodels.ChatCompletion{chatCompletion}),
+			}, nil
+		}
+
+		out := new(bytes.Buffer)
+		cfg := command.NewConfig(out, out, client, true, 100)
+		runCmd := NewRunCommand(cfg)
+
+		// End setup.
+		// ---
+		// We're finally ready to start making assertions.
+
+		// Test case 1: with no flags, the model params come from the YAML file
+		runCmd.SetArgs([]string{
+			"--file", tmp.Name(),
+		})
+
+		_, err = runCmd.ExecuteC()
+		require.NoError(t, err)
+
+		require.Equal(t, "openai/example-model", capturedReq.Model)
+		require.Equal(t, 300, *capturedReq.MaxTokens)
+		require.Equal(t, 0.8, *capturedReq.Temperature)
+		require.Equal(t, 0.9, *capturedReq.TopP)
+
+		require.Equal(t, "System message", *capturedReq.Messages[0].Content)
+		require.Equal(t, "User message", *capturedReq.Messages[1].Content)
+
+		// Hooray!
+		// Test case 2: values from flags override the params from the YAML file
+		runCmd = NewRunCommand(cfg)
+		runCmd.SetArgs([]string{
+			"openai/example-model-4o-mini-plus",
+			"--file", tmp.Name(),
+			"--max-tokens", "150",
+			"--temperature", "0.1",
+			"--top-p", "0.3",
+		})
+
+		_, err = runCmd.ExecuteC()
+		require.NoError(t, err)
+
+		require.Equal(t, "openai/example-model-4o-mini-plus", capturedReq.Model)
+		require.Equal(t, 150, *capturedReq.MaxTokens)
+		require.Equal(t, 0.1, *capturedReq.Temperature)
+		require.Equal(t, 0.3, *capturedReq.TopP)
+
+		require.Equal(t, "System message", *capturedReq.Messages[0].Content)
+		require.Equal(t, "User message", *capturedReq.Messages[1].Content)
+	})
 }