A = d v / dt = (v2 - v1 ) / t
if v2 < v1, then a is negative. always....
Only possibility that a can be positive is that you choose a sign convention in such a way that quantities in the direction of movement are negative. and the quantities in the opposite direction are positive.
Choose the downward direction (vertically) as the positive y axis. If a stone is throne upwards with an initial velocity u. Then the displacement s = 0 at t = 0 and then it becomes more and more negative. Hence, velocity will be negative. As the speed reduces, change in velocity is positive ie., acceleration is positive.