Pada Desember 2004, Berkus dan pasangannya pada saat itu, fotografer Fernando Bengoechea, sedang berlibur di pantai di [[Sri Lanka]] dan kemudian terjadi [[gempa bumi dan tsunami Samudra Hindia 2004|tsunami besar]]. Berkus selamat, tetapi Bengoechea hilang dan diduga tewas.<ref>{{cite web|last=Ayers |first=Dennis |url=http://www.afterelton.com/people/2008/3/nateberkus?page=0%2C1 |title=Interview With Nate Berkus of "Oprah's Big Give" |publisher=After Elton |date=March 11, 2008 |accessdate=December 24, 2011 | archiveurl = https://web.archive.org/web/20090722034548/http://www.afterelton.com/people/2008/3/nateberkus?page=0%2C1 | archivedate=July 22, 2009}}</ref> Berkus muncul di acara ''[[The Oprah Winfrey Show]]'' pada tanggal 17 Januari 2005 untuk menceritakan penderitaannya setelah pasangannya meninggal.
Setelah satu tahun berkencan, Berkus bertunangan dengan perancang ruangan [[Jeremiah Brent]] pada April 2013.<ref>{{cite web|last1=Boehm|first1=Kristin|last2=Triggs|first2=Charlotte|url=http://www.people.com/people/article/0,,20689945,00.html|title=Nate Berkus Is Engaged to Jeremiah Brent|work=[[People (magazine)|People]]|date=April 10, 2013|access-date=2018-01-30|archive-date=2016-08-17|archive-url=https://web.archive.org/web/20160817141105/http://www.people.com/people/article/0,,20689945,00.html|dead-url=yes}}</ref> Mereka menikah pada tanggal 4 Mei 2014 di Manhattan.<ref>{{cite web|last=Webber|first=Stephanie |url=http://www.usmagazine.com/celebrity-news/news/nate-berkus-marries-fiance-jeremiah-brent-in-nyc-201435|title=Nate Berkus Marries Fiance Jeremiah Brent in NYC: New Details on Ceremony, Reception |work=Us Weekly|date=May 3, 2014|accessdate=May 5, 2014}}</ref> Anak perempuan mereka, Poppy Brent-Berkus, lahir pada tanggal 23 Maret 2015 dengan bantuan dari [[surogat]].<ref>{{cite web| url=https://www.facebook.com/NateBerkus/posts/10152709736932765 | title= Jeremiah & I are thrilled to announce...| publisher = Nate Berkus verified Facebook pager| date= March 25, 2015| accessdate= March 25, 2015}}</ref><ref>[http://www.huffingtonpost.com/2015/03/25/nate-berkus-daughter-_n_6940864.html ''Huffington Post'': Nate Berkus Welcomes A Daughter, Poppy Brent-Berkus]</ref><ref>[https://www.popsugar.com/celebrity/Nate-Berkus-Jeremiah-Brent-Cute-Family-Instagram-Pics-38357774 PopSugar: Nate Berkus and Jeremiah Brent's Snaps of Their Daughter, Poppy, Are Devastatingly Sweet]</ref> Berkus dan keluarganya saat ini menetap di [[West Hollywood, Kalifornia]].
