The application for a licence at European Food and Wine, at 36 Red Lion Street, was dismissed by Boston Borough Council after the police raised a number of objections.
The shop had its original premises licence revoked after a police raid in October last year which followed test purchase operations where illegal cigarettes were sold.
The Alcohol Licensing Team from Lincolnshire Police presented evidence that they believed demonstrated the applicant, Talib Karim, was likely to undermine the licensing objectives and the application should not proceed.
Sergeant Kim Enderby, Alcohol Licensing Manager for Lincolnshire Police, said: "This is an excellent result, and sends a strong message from the police and council to those individuals trying to obtain a premises licence.
“This is the second time the council has refused an attempt to licence this store since it had its licence revoked.
"A lot of work is undertaken by my team whenever we receive a new licence application. We will always seek to prove the application is genuine and not an attempt to disguise criminal activity.
“Any applicant will also be expected to demonstrate they understand the Licensing Act and demonstrate how they would promote the Licensing Objectives. A lot of our work goes unreported, as once we present our evidence the application is often withdrawn rather than face the scrutiny of the Licensing Sub-Committee.
"There was recently an attempt to licence a store on Boston High Street which we had concerns about, so we conducted a test purchase operation with trading standards officers, where we purchased illegal cigarettes, the store was then raided and thousands of illicit cigarettes were seized.
“Not surprisingly that application was immediately withdrawn and no further attempt has been made to obtain a licence. Where we have the evidence we will continue to robustly challenge any attempt to obtain a premises licence.”
Another application for a licence for a store at Vauxhall Bridge, was also refused recently after police submitted evidence outlining their concerns.
Sgt Enderby said: “I would also encourage people in Boston to keep supplying us with information about stores involved in criminal activity."