Hundreds of Big Apple charities are in danger of losing their properties as they struggle to keep up with the city’s onerous paperwork requirements, which include a yearly filing to maintain the exempt status.

As of the end of May, 480 properties owned by nonprofits across the five boroughs — including shelters and hospitals — owed the city a total of $54.15 million and were on a lien list.

Some $34.3 million of the money owed is in real estate taxes and $17.87 million in water bills, with other charges and emergency repairs making up the rest.

The problem is in the city’s cumbersome rules requiring charitable organizations to apply to the city’s Department of Finance to obtain a tax exemption — a process that can require a lawyer and architect and many months for review, especially if portions of the building are being used for a commercial enterprise, such as a retail store.

After an exempt status is granted, the charity has to separately apply to the Department of Environmental Protection to obtain an exemption for its water bill.

While these procedures are pending, taxes and water charges are ticking away — sometimes with interest.

Meanwhile, charities that miss deadlines or file paperwork incorrectly can find that the city isn’t willing to help them — unless and until a light is shined on the problem.

In 2017, a property owned by Overcoming-Love Ministries, a Brooklyn organization that feeds and houses homeless families, had its tax liens sold and was being foreclosed by Tower, the administrative company that collects taxes on properties that are purchased in the lien sale.

After Between the Bricks wrote about its problems, “everything changed,” attorney David Fiveson said last week.

“You did it. The city wouldn’t talk to us and now they are buying back his lien,” Fiveson said.

But Overcoming-Love Ministries’ problems are not over. With more than $4.57 million due on another property, the Brooklyn homeless organization tops a list of 480 nonprofits that missed paperwork and have properties that could be sold in a lien sale.

The organization, whose top executive died last year, did not return a call for comment.

Overcoming-Love Ministries’ four-story building at 246 Jamaica Ave. in Brooklyn was purchased by an LLC controlled by the late Rev. Leopoldo Karl in 1980.

Over the next decade it was taken by the city for nonpayment of taxes and other fees but, each time, the foreclosure was vacated. In June of 1999, Karl transferred the 20-unit apartment building to Overcoming-Love Ministries.

Dubbed the Van Siclen Family Residence, it was one of the shelters top-rated by the city in 2005, according to a New York Times article.

The top three delinquent nonprofits together owe New York City more than $12.6 million, while the next two, Brooklyn’s Brookdale University Hospital Medical Center at 1275 Linden Blvd. and the Kingsbrook Jewish Medical Center at 585 Schenectady Ave., owe $6.6 million just in water bills.

The two hospitals reached an agreement with the city’s water board in 2015 to pay down this debt. They did not return requests for comment.

The list shows Maimonides Medical Center owing more than $643,400, including $105,250 in water bills for a 98-unit apartment building at 926 49th St. in Brooklyn that houses its interns and offices.

The hospital owns numerous properties, and a Maimonides spokeswoman was surprised the city’s online bill status still shows the outstanding debt, as its nonprofit status was restored in May by the Department of Finance and an application is pending with the Department of Environmental Protection for its water.

Jeffrey Shear, the Department of Finance deputy commissioner for treasury, payments and operations, says that owners and organizations must pay up, provide documents to confirm their exempt status or sign an agreement to pay by July 19 — as liens will be sold on Aug. 2.