Naldo made his professional debut on 7 May 2010, coming on as a late substitute in a 1–1 away draw against ASA de Arapiraca.[6] He scored his first goal on 3 September, netting the last in a 3–1 win at América Mineiro.[7]
On 29 December 2010, Naldo moved to Cruzeiro EC, in Série A.[8] After featuring regularly for the club he moved to fellow league team Grêmio FBPA on 9 January 2012.[9]
On 29 January 2013, Naldo signed a five-year deal with Granada CF, being immediately loaned to Serie A's Bologna F.C. 1909.[10] He made his debut in the competition on 10 March, playing the entire second half in a 1–0 away win against Inter Milan.[11]
In May 2013, after making five appearances for Bologna, Naldo was assigned to Granada's partner club Udinese Calcio.[12] A backup to countryman Danilo and Thomas Heurtaux, he appeared in 16 matches during the campaign.
On 1 September 2014, Naldo was loaned to La Liga side Getafe CF, in a season-long deal.[13] He made his debut in the competition on the 14th, starting in a 2–0 away loss against Sevilla FC.[14]
On 18 July 2015, Naldo signed for Portuguese side Sporting CP, but moved to Russian club FC Krasnodar on 26 August of the following year.[15] On 10 August 2017, Krasnodar confirmed his transfer to RCD Espanyol.[16]
On 25 July 2022, after two years at Turkish side Antalyaspor, Naldo joined Saudi Arabian club Al-Taawoun on a free transfer.[17] On 18 August of the following year, he returned to Antalyaspor for one year with an option for a second year.[18]
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