Lyngdoh signed for Shillong Lajong in 2011 from Rangdajied United, who were then known as Ar-Hima, for whom he was the captain in the last season. He would finish as the top scorer for Lajong during the 2011-12 I-League scoring 4 times. He would then go on to make 23 I-League appearances for Lajong during the 2012-13 I-League season.
Rangdajied United
After spending 2 years with Shillong Lajong, Lyngdoh re-signed for Rangdajied United and made his debut in the I-League on 22 September 2013 against Prayag United at the Salt Lake Stadium, playing the full match as Rangdajied lost 0–2. He would make 19 I-League appearances for Rangdajied.
In July 2014 Lyngdoh signed a one-year deal with I-League winners Bengaluru FC. Lyngdoh scored his first goal for Bengaluru during the 2014 Durand Cup, in a game against Mohammedan. Eugene would then score his second goal in the 2014–15 Federation Cup semi-final against Sporting Goa in a 3–0 win. Eugene kept up his high level of performances and scored Bengaluru FC's first goal of the 2014-15 I-League in a disappointing 1–3 defeat at home to Pune, with an outstanding finish. He would score again, this time in the 4th round of the season against Royal Wahingdoh in a 4–0 away win in Shillong. Eugene would then create history by scoring Bengaluru FC's first ever goal in Asian continental club competition in an AFC Champions League qualifier against Johor Darul Ta'zim of Malaysia in a 2–1 loss, directly from a corner. By scoring against Johor, he became the first player from an I-League club to score in all four club competitions in the season. He would assist club captain Sunil Chhetri during an away game at Mohun Bagan for Bengaluru's opener, but couldn't prevent his team from going down 4–1 at Kolkata. Lyngdoh would assist Josh Walker in a 4–1 win against Sporting Goa on 31 March 2015 with a free-kick into the box, which was headed in for the first goal by the latter. He continued his fine form with another assist from a free-kick into the box for Shankar Sampingiraj to head home in a thrilling 3–3 draw at home to Royal Wahingdoh on 3 April 2015. He assisted Sampingiraj again, this time against Pune on 21 April 2015 with a cross from the left before scoring with a spectacular first time shot from outside the box, and assisting C.K. Vineeth on 24 April 2015 against Bharat FC. Lyngdoh augmented his statistics for the season with an assist from a free-kick into the box for Sean Rooney to head home against Shillong Lajong in a 1–1 away draw. On 17 May 2015, Lyngdoh assisted once and scored once against Salgaocar in a crucial 3–1 win for his team. Lyngdoh was involved in the last goal his team scored of the season, in the final round against Mohun Bagan, in a title-deciding match, assisting John Johnson from a corner, but could't help his team win in the game that ended 1–1, and thus losing out on the title. Lyngdoh was rewarded for an outstanding season, where he made 33 appearances in all competitions, scoring 9 times and assisting 16 times, when he was named Bengaluru FC Fan's Player of the Year and Player's Player of the Year, as well as being named the 2014–15 I-league Midfielder of the Season. Lyngdoh signed a 2-year extension to his contract that would keep him at Bengaluru FC until the end of 2016–17 season on 4 June 2015.
Lyngdoh was signed by Indian Super League club Pune City on 10 July 2015 in the player drafts for Rs. 1.05 crore for the 2015 Indian Super League. Pune City's manager David Platt praised Eugeneson for his technical ability and explained why the Pune-based franchise paid very high for his services. On 28 September 2015, he was named the "Football Player Association of India"s player of the year. Lyngdoh scored his first goal of the Indian Super League against FC Goa in his 5th game of the season, from a header in a 1–1 draw at Goa. He scored again on his 7th game of the season against FC Goa from a Didier Zokora pass. On 20 December 2015, Euegenson was voted by the coaches in the I-League as the best among the Indians, thus winning the "2015 AIFF Player of the Year".
Lyngdoh was picked up by ATK in the draft for the 2017-18 Indian Super League season. Most of his time in the club was on the bench due to injury. The club decided to make a mutual contract termination, which materialised on 13 June 2019 between ATK and Lyngdoh.
