The move was agreed in 2016 after Russia's annexation of Crimea from Ukraine two years earlier.
It also comes with continuing and growing concerns about Russian aggression along Estonia's border.
Barry Mitchell is Pastor of the Living Waters Church in the country's capital Tallinn.
He's told Premier he's pleased:
"Our little army would not be able to do anything, so any support, from the UK, States and any other country that sends troops to this part of the world brings more confidence that we are not alone and that there would be support if it was ever needed.
"I have always believed that one of the greatest powers that we have is the power of prayer. As a pastor here I believe in prayer and it's just been God's hand that is over us.
"I believe that is why I am here and why others are here although there aren't too many believers here at this time I think there will be a shift in that soon.
"My message is just a positive message and to keep your faith in God."
The deployment has also featured in the General Election campaign.
During a visit to Estonia to meet British troops sent to the border in the face of increasing Russian aggression, the Tory Cabinet minister condemned Labour leader Jeremy Corbyn for raising concerns about the deployment.
Sir Michael told reporters: "Russia will be watching Labour's feebleness. Jeremy Corbyn has not supported this deployment. He has questioned it."
He also asked if he (Corbyn) would continue to support he UK's involvement with, and contribution to, NATO.
In January, Mr Corbyn said no more British troops should be sent to the Baltic states and called for increased dialogue with Russia.
The Labour leader also refused to say if he agreed with the Nato principle of collective defence - which means an attack on one member is deemed an attack on all.
Mr Corbyn's spokesman had previously suggested Britain's deployment of troops and jets to Estonia was escalating tensions with Moscow.
Sir Michael insisted the UK would stand with its allies in the region.
"The troops I have met today are part of one of the UK's largest ever deployments to Eastern Europe," he said.
"This marks our commitment to European security and standing with our allies in the face of an increasingly assertive Russia."
An RAF Typhoon aircraft is being sent to Romania in the next few weeks to carry out a Nato air policing mission in the Black Sea.