Here’s how to change MySQL Workbench’s colors (INCLUDING THE BACKGROUND COLOR).
Open the XML file called code_editor.xml located in the data folder of the MySQL Workbench’s installation directory (usually C:\Program Files\MySQL\MySQL Workbench 6.3 CE\data). Here you’ll find a lot of styling for different code elements, but there are some missing.
MySQL Workbench uses scintilla as the code editor, and scintilla defines a few more styles that you can use in the code_editor.xml file. The one that is used for the background color is style id 32.
Here’s the complete list for MySQL (scintilla has thousands of styles for many languages) with my configuration:
<style id= "0" fore-color="#DDDDDD" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_DEFAULT -->
<style id= "1" fore-color="#999999" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_COMMENT -->
<style id= "2" fore-color="#999999" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_COMMENTLINE -->
<style id= "3" fore-color="#DDDDDD" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_VARIABLE -->
<style id= "4" fore-color="#9B859D" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_SYSTEMVARIABLE -->
<style id= "5" fore-color="#9B859D" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_KNOWNSYSTEMVARIABLE -->
<style id= "6" fore-color="#FF8080" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_NUMBER -->
<style id= "7" fore-color="#7AAAD7" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_MAJORKEYWORD -->
<style id= "8" fore-color="#7AAAD7" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_KEYWORD -->
<style id= "9" fore-color="#9B859D" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_DATABASEOBJECT -->
<style id="10" fore-color="#DDDDDD" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_PROCEDUREKEYWORD -->
<style id="11" fore-color="#B9CB89" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_STRING -->
<style id="12" fore-color="#B9CB89" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_SQSTRING -->
<style id="13" fore-color="#B9CB89" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_DQSTRING -->
<style id="14" fore-color="#FFBB80" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_OPERATOR -->
<style id="15" fore-color="#9B859D" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_FUNCTION -->
<style id="16" fore-color="#DDDDDD" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_IDENTIFIER -->
<style id="17" fore-color="#B9CB89" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_QUOTEDIDENTIFIER -->
<style id="18" fore-color="#B9CB89" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_USER1 -->
<style id="19" fore-color="#B9CB89" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_USER2 -->
<style id="20" fore-color="#B9CB89" back-color="#2A2A2A" bold="No" /> <!-- SCE_MYSQL_USER3 -->
<style id="21" fore-color="#FFBB80" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_HIDDENCOMMAND -->
<style id="22" fore-color="#909090" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_PLACEHOLDER -->
<!-- These two are for scintilla globally. -->
<style id="32" fore-color="#DDDDDD" back-color="#2A2A2A" bold="No" /> <!-- STYLE_DEFAULT THIS IS THE ONE FOR THE BACKGROUND!!!!! -->
<style id="33" fore-color="#2A2A2A" back-color="#DDDDDD" bold="No" /> <!-- STYLE_LINENUMBER -->
<!-- All styles again in their variant in a hidden command (with a 0x40 offset). -->
<style id="65" fore-color="#999999" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_COMMENT -->
<style id="66" fore-color="#999999" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_COMMENTLINE -->
<style id="67" fore-color="#DDDDDD" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_VARIABLE -->
<style id="68" fore-color="#9B859D" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_SYSTEMVARIABLE -->
<style id="69" fore-color="#9B859D" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_KNOWNSYSTEMVARIABLE -->
<style id="70" fore-color="#FF8080" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_NUMBER -->
<style id="71" fore-color="#7AAAD7" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_MAJORKEYWORD -->
<style id="72" fore-color="#7AAAD7" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_KEYWORD -->
<style id="73" fore-color="#9B859D" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_DATABASEOBJECT -->
<style id="74" fore-color="#DDDDDD" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_PROCEDUREKEYWORD -->
<style id="75" fore-color="#B9CB89" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_STRING -->
<style id="76" fore-color="#B9CB89" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_SQSTRING -->
<style id="77" fore-color="#B9CB89" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_DQSTRING -->
<style id="78" fore-color="#FFBB80" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_OPERATOR -->
<style id="79" fore-color="#9B859D" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_FUNCTION -->
<style id="80" fore-color="#DDDDDD" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_IDENTIFIER -->
<style id="81" fore-color="#B9CB89" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_QUOTEDIDENTIFIER -->
<style id="82" fore-color="#B9CB89" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_USER1 -->
<style id="83" fore-color="#B9CB89" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_USER2 -->
<style id="84" fore-color="#B9CB89" back-color="#707070" bold="No" /> <!-- SCE_MYSQL_USER3 -->
<style id="85" fore-color="#FFBB80" back-color="#909090" bold="No" /> <!-- SCE_MYSQL_HIDDENCOMMAND -->
<style id="86" fore-color="#AAAAAA" back-color="#909090" bold="No" /> <!-- SCE_MYSQL_PLACEHOLDER -->