Manchester City forward Mebude, 18, fired in a terrific drive after nine minutes but Hugo Larsson levelled from close range five minutes later.
The Swedes stepped it up after the break and Otto Rosengren scored with a well-worked goal in the 58th minute before 17-year-old substitute Roony Bardghji – Sweden’s rising star – drove in a terrific third with five minutes remaining.
Lewis Fiorini pulled a goal back for the young Scots with a wonderful strike at the death.
Scot Gemmill’s side play Wales on Sunday in the second of their double-header, part of their preparations for the UEFA Euro 2025 Under-21 Championship qualifying campaign which begins in September, and they can take some positives, especially from the first-half performance.
Scotland’s opener was class. Ex-Rangers youngster Mebude took a pass from Fiorini, twisted and turned just inside the Sweden box before flashing a low drive past goalkeeper Noel Tornqvist. Four minutes later, Celtic’s Ben Summers, another 18-year-old debutant, drove wide from 20 yards after linking up with Mebude.
Sweden, who had threatened on the break, fought back and when captain Omar Faraj got on the end of a deep cross and headed to the back post, Larsson was all alone to knock the ball past Scotland goalkeeper Cieran Slicker.
Just before the break, on a Sweden counter, Sebastian Nanasi hit the crossbar with a curling shot from 20 yards before Faraj drove the rebound wide.
The young Swedes started the second half better and just before the hour they forged ahead. Rosengren drove forward, laid the ball off to left-back Noah Persson and continued on to take the return pass before driving the ball low past Slicker from 12 yards.
Substitutes, as expected, came on to disrupt the flow. Bardghji forced a fine save from Slicker when he swept in a shot from another Persson cutback and Scotland survived a couple of corners.
More Sweden substitutes came on to make an impact. Jacob Ondrejka came close with a drive and Slicker saved from a smart Daniel Svensson shot before Bardghji took a pass from Josaphat Mendes and hammered the ball past Slicker from 14 yards.
However, the best goal of the night came right at the end when Fiorini volleyed in from outside the box from a corner to end the night on a positive for the Scots.