The first upgrade costs 750. It reduces the engineer tower and upgrade price by 5%.
The second upgrade costs 750. It increases the engineer attack speed by 10%.
The third upgrade costs 1250 (1000 in Mobile). It allows itself and the turrets to pop lead and frozen bloons.
(Bloons TD 5 Mobile exclusive) The fourth upgrade costs 1500. Once you buy and activate this, the engineer will build "super sentries". These are bigger sentries that shoot faster and will last longer before being destroyed.
Super Sentries fire twice as fast as normal sentries (3 shots per second vs 1.5), and last 50% longer (37.5 seconds vs 25). However, super sentries are built half as fast compared to normal sentries (every 20 seconds vs every 10, 6 with Fast Engineering). This means Engineers can now only have two super-sentries up at a time, lowering the purpose of the upgrade. The super sentries also aren't affected by Fast Engineering, making the upgrade worthless unless if it's to purchase Cleansing Foam or Bloon Trap.
There used to be no Bloonchipper in BTD5 iOS, making the Engineer's Workshop not decrease any towers' prices and upgrades, making this Specialty Building have a greater advantage.
This is not true as of version 2.2, as it now makes Bloonchippers more expensive.