Goals from Rob Hulse and Lee Bell earned Crewe their first victory of the Nationwide Division Two campaign.
But it was far from convincing stuff against a Colchester side that played some pretty football without any end product.
Hulse put Crewe on their way in ninth minute when he took Dean Ashton's pull back from the byline in his stride and shot into the roof of the net and the near post.
Hulse also shot wide and Efe Sodje headed over the bar from a corner kick as Crewe controlled the first 20 minutes.
But the U's hit back and striker Scott McGleish came close with a downward header from Mick Stockwell's cross which was beaten out by home keeper Clayton Ince.
Colchester were enterprising with much of their play but lacked the cutting edge. Dean Morgan spun away from Sagi Burton but sliced his effort from 15 yards over the bar and Thomas Pinault threatened on several occasions.
The home side needed a second to make sure of the three points. They came close when Ashton crashed a right-footed shot on to the top of the post in the 76th minute.
But then substitute Bell wrapped up the win when he took Ashton's layoff just outside the box and rifled a rising drive into the top corner past Keeper Richard McKinney.
Crewe boss Dario Grady admitted "We have played outstanding football in our first two games and got little to show from it, but we played much worse today and still got three points. I thought it was important to get a win and we needed to go a little bit more direct in our play."
Colchester manager Steve Whitton criticized his forwards for being lethargic.
"We had so much possession of the ball but the final cutting edge wasn't there and the forwards looked a bit stale. We were not positive enough in the final third."