I will be starting a new job in July and I will need to fill out a W4.
My spouse earns higher than me and he is an independent contractor and is on 1099.
I was unsure of how many allowances to claim?
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It depends. I know that's not helpful, but it really does. At one extreme, you could have enough withheld to cover both you and your spouse's tax liability. At the other, you could withhold enough to cover your own, and have your spouse pay estimated taxes. Or do something in the middle.
What you really need to do is figure out how much tax the two of you expect to owe, and make sure the IRS gets that amount*. They won't really care what way you do it, as long as they get the money in a relatively timely fashion - that is, if the spouse earns evenly throughout the year, but pays the estimated tax for that amount in the last quarter (and nothing the other 3 quarters), it may raise some red flags.
*Note the "safe harbor" provision, where if you pay an amount equal to last year's tax, you don't incur penalties even if this year's tax is more. (Check the IRS for exact provisions.)