Change CSS at RUNTIME : http://stackoverflow.com/questions/24762217/edit-javafx-css-at-runtime

CSSController.java

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.net.URL;
import java.util.ResourceBundle;

import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.fxml.FXML;
import javafx.fxml.Initializable;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.TextArea;

public class CSSController implements Initializable{
    private Scene scene;
    @FXML TextArea cssContent;
    @FXML Button defineCSSButton;
    @Override
    public void initialize(URL location, ResourceBundle resources) {
        defineCSSButton.setOnAction(new EventHandler<ActionEvent>(){
            @Override
            public void handle(ActionEvent event) {
                String css = cssContent.getText();
                try{
                    File temp = new File("tempfile.css"); 
                    temp.delete();
                    temp.createNewFile();
                    BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
                    bw.write(css);
                    bw.close();
                    String url = "tempfile.css";
                    scene.getStylesheets().add(temp.toURI().toString());
                }catch(Exception e){
                    e.printStackTrace();
                }
            }
        });    
    }
    public void setScene(Scene scene) { this.scene = scene; }
}

doc.fxml

<?xml version="1.0" encoding="UTF-8"?>

<?import java.lang.*?>
<?import javafx.scene.control.*?>
<?import javafx.scene.layout.*?>
<?import javafx.scene.shape.*?>

<AnchorPane maxHeight="-Infinity" maxWidth="-Infinity"
	minHeight="-Infinity" minWidth="-Infinity" prefHeight="400.0"
	prefWidth="600.0" xmlns="http://javafx.com/javafx/8" xmlns:fx="http://javafx.com/fxml/1" fx:controller="CSSController">
	<children>
		<TextArea fx:id="cssContent" layoutX="14.0" layoutY="26.0"
			prefHeight="292.0" prefWidth="319.0" />
		<Label layoutX="22.0" layoutY="6.0" text="Define your CSS here:" />
		<Button fx:id="defineCSSButton" layoutX="14.1875" layoutY="333.5"
			mnemonicParsing="false" text="Define CSS" />
		<Line endY="400.0" layoutX="332.0" />
		<Label layoutX="418.0" layoutY="15.0" text="Components:" />
		<ChoiceBox layoutX="343.0" layoutY="48.0" prefWidth="150.0" />
		<ColorPicker layoutX="343.3759765625" layoutY="86.0" />
		<CheckBox layoutX="347.6650390625" layoutY="123.0"
			mnemonicParsing="false" text="CheckBox" />
		<MenuButton layoutX="343.37109375" layoutY="159.5"
			mnemonicParsing="false" text="MenuButton">
			<items>
				<MenuItem mnemonicParsing="false" text="Action 1" />
				<MenuItem mnemonicParsing="false" text="Unspecified Action" />
				<MenuItem mnemonicParsing="false" text="Unspecified Action" />
				<CheckMenuItem mnemonicParsing="false" text="Unspecified Action" />
			</items>
		</MenuButton>
		<ProgressIndicator layoutX="347.9091796875" layoutY="200.01953125"
			progress="0.0" />
		<Slider layoutX="410.0" layoutY="213.01953125" />
		<ToggleButton layoutX="348.7421875" layoutY="254.0"
			mnemonicParsing="false" text="ToggleButton" />
	</children>
</AnchorPane>

Test.java

import javafx.application.Application;
import javafx.fxml.FXMLLoader;
import javafx.scene.Parent;
import javafx.scene.Scene;
import javafx.stage.Stage;

public class Test extends Application{
    
    @Override
    public void start(Stage primaryStage) throws Exception {
        FXMLLoader loader = new FXMLLoader(getClass().getResource("doc.fxml"));
        Parent root = (Parent)loader.load();
        CSSController myController = loader.getController();
        Scene scene = new Scene(root);
        myController.setScene(scene);
        primaryStage.setScene(scene);
        primaryStage.show();
    }
    public static void main(String[] args) {
        launch(args);
    }

}