Hi,
I'm working with a multinational company in Malaysia, which has its headquarter located in California. I'm using L1 visa to work offsite in one of the site in California. I'm paid in Malaysia dollars, without any living/food/etc expenses in California, due to the reason that this trip was requested by me to work off-site for a couple of months as my spouse is relocating to work in the States. My boss requested me to use L1 visa as I'm not able to go on-leave for a couple of months. Does anybody know how much will I be taxed if my working duration is more than 90 days? How does the Tax calculation work in California? I was informed that I will get taxed if my total income exceed USD5k after 90 days. Is the income calculated starting from the first month of my stay or the 4th month onwards?

On L1, you must pay SS tax, Medicare tax and federal and state income taxes. Even if you are in U.S. for a short duration, your income paid by U.S. company may be exempt under tax treaty.