Source: S&P Dow Jones Indices
Microsoft's recovery has been slow and steady. "If you look back over the last four years, it's hard to sneeze at how well it's done ever since [CEO Satya] Nadella came in and changed the focus," said Paul Hickey, co-founder of Bespoke. "It was able to reinvent itself and successfully."
Apple was worth $826.8 billion Tuesday afternoon, while Microsoft was at $822.4 billion. On Wednesday afternoon, they were bout around $850 billion. Apple has been crushed recently by worries about iPhone sales and the tech sell-off, just months after it surpassed the $1 trillion mark.
Ironically, when Microsoft was on top in December 1999, it was worth $604 billion, while Apple was a slender $16.5 billion, according to S&P Dow Jones Indices data. Microsoft was number one again in 2002, after the tech bubble burst but with a much smaller market value of $276.4 billion.
Hickey said Microsoft isn't getting the credit it deserves. "We've seen companies like IBM and GE that haven't been able to withstand changes in the overall business environment," he said. "Microsoft is working on the whole subscription business ... and it's really getting in front of trends."
Apple has been the biggest company by market cap, since 2012, based on year-end data from S&P Dow Jones Indices. Apple and Amazon had been battling it out for No. 1, but the online retailer's stock decline in the tech swoon has left its market cap at $773.27 billion as of Tuesday's close.
Even if Microsoft surpasses Apple, the software company does not have the market sway of Apple, which has impacted sentiment and trades with the momentum names in tech. Apple has fallen 22.8 percent since Oct. 1, and Microsoft is down just 6.3 percent in that period.
"Microsoft has just been slowly going on in the background there, and almost under people's radar. It's down but it's held up better than the market. It didn't get caught up in all the excitement we saw in a lot of other stocks," said Hickey. "You look at both of them. They have identical dividend yields right now, 1.7 percent."
Hickey said it's really not unusual for a stock to fall out of favor, and now it's Apple's turn, something that it has experienced before.
Watch: Steve Jobs explains the iPhone in 2007 CNBC interview