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Bearing in mind that the Apache Cordova transforms HTML5 + CSS + Javascript into native code, you will have to make an adaptation of the basic original code to change the color of the NavigationBarColor. Below follows two forms, both via XML and programmatically, using JAVA. See:
XML
<item name="android:navigationBarColor">@color/theme_color</item>
JAVA
window.setNavigationBarColor(@ColorInt int color)
However there are some plugins in which you may be using. As for example, the Cordova-plugin-navigationbar-color. Since you are open source, you can study and adapt according to your needs. See how it would look:
window.NavigationBar.backgroundColorByHexString('#3F51B5');
Note: the method has been introduced into Android Lollipop and will not work in API version < 21.

interesting I will test
– Jefferson Mello Olynyki
could you cite an example of how to use ? in which xml I put this property, in config.xml ? , and meto there, is javascript ? how can I change to color : #3F51B5
– Jefferson Mello Olynyki
@Jeffersonmelloolynyki You came to install this plugin?
– viana
yes, I’ve installed it
– Jefferson Mello Olynyki
@Jeffersonmelloolynyki take a look at this file here, where the guy makes the change using the plugin: https://github.com/fagundes/cordova-plugin-navigationbar/blob/master/www/navigationbar.js
– viana
perfect @Ack Lay window.NavigationBar.backgroundColorByHexString('#3F51B5'); Thanks !
– Jefferson Mello Olynyki
@Jeffersonmelloolynyki edited the answer and put your code there because it can help other people. Abs. Good luck.
– viana
opa, beauty, it will help that you are with doubts, thank you
– Jefferson Mello Olynyki