As the technology becomes mainstream, the goal is to have these messages personalized for each consumer to further improve the shopping experience.
Though many beacon networks are still in pilot tests, inMarket and proximity marketing firm Mobiquity, both say there are signs that the devices are boosting both sales and the desire to make a purchase.
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"We're finding people … are taking it very seriously because it's a very timely message," said Paul Bauersfeld, chief technology officer at Mobiquity Networks. "We're seeing much higher conversion rates from [beacon] advertising than the industry has seen traditionally in just display advertising on web and email."
While implementation of the beacon technology is still in early stages, industry research suggests it could help retailers struggling with declining traffic and sales.
A study conducted by beacon platform Swirl found that 73 percent of shoppers who received a beacon-triggered message on their smartphone said it increased their likelihood of making a purchase during a store visit, while 61 percent said the message would prompt them to visit the store more often.
This year, beacon-influenced, in-store sales are projected to be $4.1 billion for the top-100 U.S. retailers, but are expected to grow to $44.1 billion in 2016—about 1 percent of total U.S. store sales, according to BI Intelligence.
The challenge, however, is delivering a relevant message at exactly the right time to persuade a customer to visit a specific retailer and, once there, to make a purchase.
"We have safeguards in place to make sure the messaging that's delivered is going to be of value to you as the consumer. That you're going to find it interesting because you're in this shoe department and you're interested in shoes and you get an offer for 20 percent off," said Thygesen.
But until then, retailers and beacon network providers are tiptoeing through the data gleaned from users to avoid app deletion.
"One message from an app I trust reminding me about my shopping list or about recipes is helpful, and I can either click on the message or dismiss it. That's like a polite welcome to the store," said Dipaola. However, "too many of those messages is almost like the greeter following you around the store."
And that's exactly what retailers want to avoid.
—CNBC's Courtney Reagan contributed to this report.