The Russian team also piled on the agony for the winless Dutchmen, who dropped their fifth game in the competition.
The home side, which won the first encounter between the two sides 78-69 in the Netherlands back on December 1, will next week travel to Italy to face Scavolini Pesaro looking to win for the sixth time in a row in Europe.
Krasnye Krylia had already booked their place in the Last 16 while Amsterdam had no chance of advancing.
The Dutch outfit did lead 20-18 midway through the second quarter but Evgeny Voronov dunked and Andrey Ivanov buried a three-pointer to put Krasnye Krylia in front to stay.
In Tuesday's rout, Ralph Biggs played big for the winners with a game-high 14 points.
He buried four of five shots from long range.
Andrey Ivanov finished with 12 points, Evgeny Voronov 11 and Luis Flores nine.
Sergei Mokin's men out-rebounded Amsterdam 46-23.
Ferdinandus Steenmets, Amsterdam coach:
"Today both teams played from [the]defense. We didn't have many opportunities to take open shots. I can say that in the first half we were more confident, but in the second we missed a lot of points after rebounding. This game against Samara is a very valuable experience for our team."
Sergey Mokin, Krasnye Krylia coach:
"We outrebounded Amsterdam; we were especially prepared for this. It is also true that Amsterdam didn't have much choice on their bench. I'd like to wish them success in their national league. As for us, we've got plenty of work in front of us."
Andrey Ivanov, Krasnye Krylia:
"The game was very difficult, we are not in our best physical shape as we're just back from the holiday season. But we played a real team game and took more rebounds, that was the key to victory."
Dimeo van der Horst, Amsterdam:
"We lost almost all the rebounds we could. We played good defense in the first half of the game, but then something went terribly wrong and we lost the match."