Due to the topography of the area, Hideyoshi determined that he could not easily burn this fortress as he had the Negoro-ji; he decided to instead use flood tactics, as he had three years earlier in the siege of Takamatsu.

The presence of the Ikki zealots was already straining Ōta's supplies of food and other resources even before the siege began.

At one point, part of the dike gave out, resulting in the drowning deaths of several of Hideyoshi's men.

However, by the 22nd day of the fourth lunar month, the garrison could hold out no longer and surrendered; fifty samurai committed seppuku.

As Hideyoshi took over the castle, he ordered all those from samurai families killed, while peasants were simply disarmed of all weapons, and sent back to their lords' fields.