The Dow and S&P 500 finished near session lows as investors were reluctant to jump in following a three-day rally, but major averages still capped the volatile quarter with gains.
Stocks finished lower for the month of June, logging their first monthly drop this year. But all three major averages logged their third winning quarter in four. And so far for the year, the Dow has surged more than 14 percent, while the S&P 500 and Nasdaq have spiked more than 13 percent each.
The Dow Jones Industrial Average declined 114.89 points to close at 14,909.60, pulling back after logging its third-straight day higher. Still, the Dow posted its strongest first half of the year since 1999.
The S&P 500 fell 6.92 points to finish at 1,606.28. The S&P 500 logged its best first half performance since 1998. The Nasdaq eked out a gain of 1.38 points to end at 3,403.25.
The CBOE Volatility Index (VIX), widely considered the best gauge of fear in the market, finished unchanged below 17.
For the quarter, the Dow rose 2.27 percent, the S&P 500 climbed 2.36 percent, and the Nasdaq soared 4.15 percent. Microsoft was the best performer for the quarter on the Dow, while IBM tumbled.
Financials topped the S&P 500 sector gainers in the second quarter, while utilities lagged.
Stocks initially opened in negative territory after Fed Governor Jeremy Stein highlighted the upcoming September policy meeting as a possible time when the central bank may need to consider paring back its QE program, adding that the Fed consider the overall economic improvements since it launched the stimulus instead of giving undue weight to the most recent round of tepid economic data.
(Read More: Buckle Up! Expect More Market Volatility This Year)
Stein's comments contradicted comments from other Fed policymakers who have suggested the central bank will bide its time before scaling back its bond purchases.
Menawhile, Richmond Fed President Jeffrey Lacker said markets should brace for more volatility as they digest news the Fed will scale back bond buying later this year, but the swings will not derail growth. Lacker said he expects U.S. growth to remain around 2 percent for the "foreseeable future."
(Read More: Fed Out in Force as Markets Stabilize)
On the economic front, business activity index in the Midwest fell in June to 51.6 from 58.7 in May, according to the Institute for Supply Management-Chicago. A Reuters survey of economists on average expected a median reading of 56.0 in June versus the May figure of 58.7.
Meanwhile, consumer sentiment improved in late June, with the final reading on the overall index at 84.1, above the preliminary reading of 82.7, according to Thomson Reuters/University of Michigan. Economists polled by Reuters had forecast the final June reading of 82.8.
Japan's benchmark stock index hit a three-week high on the heels of positive economic reports that include much stronger than expected industrial output and retail sales numbers.
"We had better job market numbers, better production numbers, and even consumer prices are picking up. So data-wise, today is a pretty good day for Japan," said Takuji Okubo, principal and chief economist at Japan Macro Advisors.
BlackBerry plunged more than 25 percent after the Canadian smartphone maker posted an unexpected loss and offered few signs of a long-promised turnaround.
Accenture dropped sharply to lead the S&P 500 laggards after the company slashed its full-year outlook. Shares of rival IBM also declined, putting downward pressure on the Dow.
Nike posted earnings that beat forecasts, but shares declined after the sports apparel retailer said it expects lower China revenue during the first half of its new fiscal year and sees first-quarter gross margins to be "essentially flat."
Noodles & Co surged more than 100 percent after its IPO priced above expectations, valuing the operator of pasta, salad and sandwich shops at about $969 million.
Traders will closely watch gold prices, as the precious metal dipped below a key level of $1,200 per ounce. Analysts warned that miners could be severely affected if prices remain this low.
(Read More: Three Reasons Gold Will Go to $800)
—By CNBC's JeeYeon Park (Follow JeeYeon on Twitter: @JeeYeonParkCNBC)
On Tap Next Week:
MONDAY: PMI manufacturing index, ISM mfg index, Amazon sales tax in NJ, Croatia joins EU
TUESDAY: Factory orders, auto sales, Fed Board of Governors mtg; Earnings from Constellation Brands
WEDNESDAY: MBA mortgage applications, Challenger job-cut report, ADP employment report, international trade, ISM non-mfg index, oil inventories, natural gas inventories, NYSE early close at 1pm ET
THURSDAY: INDEPENDENCE DAY -- MARKETS CLOSED
FRIDAY: Employment situation, jobless claims, mid-year stress tests due
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